Miss Honey acts as a Mama Bear for Matilda, but she seems to accept the abuse Aunt Trunchbull bestowed on her with stoic resignation. Part of the reason is that she sees great potential in Matilda, the grace and confidence that Trunchbull squelched in Miss Honey when the latter was a child, and part of it is knowing what it's like to have the world tear away that confidence. Miss Honey in both the book and movie doesn't believe that she deserves better in life, since she doesn't actively fight for the things she deserves like her inheritance or her wages. Seeing Matilda risk experiencing the same thing, though, from Miss Trunchbull and the Wormwoods? For Miss Honey, it becomes a case of We Are Not Going Through That Again and You Are Better Than You Think You Are.
In the movie, the Wormwoods go to Guam to get away from the FBI. Guam is a territory of the U.S. and the FBI would certainly be able to find them there. But, since they are incredibly stupid, TV-watching slobs, they probably didn't think of that point for one second. (Of course, that's assuming they were telling the truth about their planned destination.)
When Matilda says "whoever painted the Trunchbull must have had a really strong stomach," she means "It's amazing that someone was able to complete a painting of the Trunchbull without throwing up."
Why does Matilda dispose of evidence when the FBI search the house? We know from the narrator that at least part of the reason is Matilda's futile hope that Harry will eventually see the error of his ways, which be could only do if he's still a free man. But a better and more pragmatic reason is Matilda knows that if her parents are arrested, she'll be put into foster care probably away from her friends and Miss Honey. And her plan is for Miss Honey to adopt her.
The Trunchbull notably doesn't do anything when Miss Honey frees Matilda from the chokey. Foreshadowing that she's just a bully and she'll be powerless once the school stands up to her.
Matilda's class stands up to the Tunchbull. Just before everyone gets sent to Chokey, Matilda writes on the chalkboard as Magnus. The Trunchbull is never seen again, and the schoolkids sing Revolting Children, which includes the two lines "And we won't forget the day we fought/for the right to be a little bit naughty". An audience member knows Matilda had to piece a lot of clues together, and use her powers to defeat the Trunchbull. But the kids don't. They're in the youngest class, and managed to stand up to the Trunchbull. Just when things were looking bad for them, "Magnus" showed up and placed the straw that broke the camel's back. So they've just worked with a ghost to achieve the impossible. Fought for the right, indeed.
The blackboard scene is taken straight from the book but it's even more appropriate here. In the book Ms. Trunchbull only thought she was seeing a ghost. However in the musical it's implied that Matilda was either possessed or communing with Magnus. So effectively yes it WAS Magnus enacting his revenge. This would also explain why Matilda lost her powers. Magnus moved on and thus Matilda had no power other than her own mind.
Even better, the word 'Magnus' is a title given to a powerful magician. Badass from beyond the grave, anyone?
How's this; if Magnus was the reason for Matilda's power, that explains why Matilda knows his and his family's story, as well as why Matilda hears these stories and thoughts seemingly out of her control, like in "Quiet". That all is one of the main reasons the theory is so profound in this version. But think; the story Matilda tells has a lot of very silly or unrealistic moments: the name of the dangerous act, some of the more fantastical elements of the Honey-Trunchbull family, and to a lesser extent, the acrobat breaking her bones instead of being impaled or bitten. But if Magnus knows he's telling the story to a little girl, he probably wants to scare her as little as possible, as well as make her and everyone else think she came up with the story. Plus, his love and devotion for his wife and hatred of Trunchbull probably tainted some of his descriptions (Granted, from what we see of Trunchbull, his descriptions of her probably aren't that far off, but still.). The trick probably had a shorter name, and just didn't have a safety net. Why did he let her see Miss Trunchbull in full force? Because she'd seen it all before, so she probably wouldn't be too scarred by a little more.
Additionally, she gains her powers both when she's at the absolute low point of her life, AND when Miss Honey is being scolded by Miss Trunchbull right in front of her. He's probably more than a little angry.
Matilda mispronounces words in the play. It's easiest to tell in the soundtrack, where she mispronounces anticipation as 'ancipation', slippery as 'slippy', atmospheric as 'atmospharic', and a few other words. (Weirdly, escapologist is pronounced exactly correct.) Note those examples are from the extremely dramatic and serious 'Story' songs, not the comedic songs where mispronunciations might be funny. And while a young actress might mispronounce words in the play, presumably someone would have caught that on the released songtrack. But these mispronunciations are entirely on purpose...because Matilda, like many very intelligent children her age, learned the words via reading them.
In the book, it is mentioned in passing that Matilda read Tess of the D'Ubervilles, which deals with the titular character having been raped. It's mentioned to highlight Matilda's status as a Child Prodigy, but still, it's more than a bit horrifying to think about a five-year-old reading something of that subject matter.
She mentions to Miss Honey that she didn't understand some of the finer points of the books she was reading, so she might not have clearly understood that aspect of the story.
Fridge, but Miss Honey might acknowledge this in universe: she is taken aback by Matilda's reading, probably not just by the fact that she is reading and has read so many books, but also the topics of some.
Also, Tess of the D'Ubervilles was written in such a way that what's happening isn't ever said directly. Instead, the reader uses their own knowledge and ability to read between the lines to work out exactly what happened. (Most of the books Matilda reads are written in the same way, incidentally.) Despite being incredibly intelligent, it's unlikely Matilda at five years old had enough worldly knowledge to work out exactly what was going on, only the very basic gist of it.
Miss Honey's story is horrific enough without any reading-between-the-lines, but older readers may notice that she actually says very little about what the Trunchbull did to her: she only said that it was too awful to talk about.
If Miss Honey's hypothesis that geniuses can develop psychokinesis just from not being challenged enough, that's actually pretty disturbing when you think about it.
If Matilda is wrong and Magnus wasn't killed by the Trunchbull, but if Miss Honey is right that it wasn't suicide, that means that his murderer may never have been caught.
Bit of a Meta example, the song "Little Bitty Pretty One" by Thurston Harris plays when Matilda learns how to control her powers. While on the surface it's a whimsical moment, on the meta level, it's the same song used when Christine goes after her first victim. And since stuff gets real later on after that montage.....
Matilda's trigger for her telekinetic abilities was being pushed around by her family and Principal Trunchbull. Late in the movie, she's using said abilities effortlessly to impress her teacher and later screw with Trunchbull. It's likely her mind developed past said trigger, but if that's not the case, Matilda HAS to remember some moment in her life where she had to take a lot of crap from someone (most likely her family) in order to access her abilities, which can be just as painful as actually experiencing the moment in question.
"Magnus" threatens to kill the Trunchbull. Except "Magnus" isMatilda! Though it's likely Matilda only intended to Scare 'Em Straight, the implication is still frightening.
Maybe a little less so when you consider that children sometimes do that as they don't understand just what the ramifications - it's not uncommon for children, especially ones Matilda's age, making death threats or threats of violence and not actually mean it because they don't understand it. Matilda very likely overheard it from the telly or even learned it from one of her books.
The book also contains a veiled death threat in the same scene ("If you don't [give Miss Honey her wages and house, and leave] [...] I will get you like you got me"), though again it's very likely that Matilda wasn't going to follow through with it.
While it's only implied, Trunchbull's terrified reaction when "Magnus" accuses her of being responsible for his death.
In a darkly sinister sort of way, all of Trunchbull's outlandish punishments are brilliant in how they help her cover up her abuse of the children, even if they largely come from her being a Roald Dahl character. The more outlandish her punishments over minor offenses, the less likely the children are believed. A parent would entirely believe and be angry over their child being hit or otherwise. But what parent would properly believe their child being thrown across the schoolyard by their hair for wearing pigtails, or being forced to eat a stomach burstingly large chocolate cake as punishment for being accused of stealing cake?