The reason why you see Charles as the killer who offed Madame Fate? It's personal; he used to be an exhibit in her carnival before sent into an asylum!
In Dire Grove there are four people representing the four elements, wind, water, fire, and earth. In the end game you use the fifth element, the silver soul, in a puzzle. This is represented by the object mercury and the Detective is the person.
Several of the carnies that were shown getting killed in Madame Fate turn out to be alive, albeit subjected to torture or conscripted by the Big Bad, in Fate's Carnival. Given that their deaths were only shown in Fate's crystal ball, it's likely that its images were metaphorical in some cases, and that other visions (specifically, the acrobat twins' Disney Villain Death) actually foretold how they'd expire in the next game rather than that night.
But what about the other visions? Dr. Goodwell isn't devoured by his own snake, Dante isn't hung by his own tongue, Franco starves to death instead of eating a horse...
Franco's may have been a metaphor that the Master Detective didn't understand. The others may simply not have happened yet.
And what about: Twyla, Lucy and Armando? They aren't shown. And Art didn't die of cigarettes, did he?
Possibly Art was drugged with tainted cigarettes to incapacitate him, then killed.
It's questionable to think that Alister would call it "Fate" to welcome the Master Detective to Ravenhearst in Key to Ravenhearst since it was Charles who built Ravenhearst Manor for Emma, but Ravenhearst Unlocked reveals that Alister used to be a noble until his lands were taken by Lord Ravenhearst. Later, he would go on to confront and capture the original Master Detective, who came to stop Alister's dark arts, within Lard Ravenhearst's lands. Thus Alister "welcomed" the current Master Detective much like he did to the original one.
In Sacred Grove, you learn that Alister was banished from the Mistwalkers for desecrating their life span ritual because he committed murder to extend his life. If he's been around since at least the 1600s and he killed his own daughter to do so...if the detective hadn't interrupted him, he might have eventually plotted to kill Charles and Victor as well. (Although this depends on how much sympathy you really feel for those two.)
Key establishes that Gwendolyn and Charlotte were Charles's biological daughters, not adoptive, and they evidently inherited the Dalimar family's madness. This doesn't bode well for Peter and Derek from Sacred Grove...
Also, Key shows us what happened to the twin girls and their grandfather Alister, and even to Charles's and Victor's dead bodies, but the twins' mother Rose and her predecessor Emma are both disturbingly absent.
One of the fill-screen puzzle locks in Unlocked takes things to a whole new level of horror if you think about it: to solve it, the Master Detective herself has to transfer five bobbing, ethereal souls into glass pipes which suck them up and use them to power the mechanism's unlocking. In other words, the Detective has to imprison and exploit the dead, in the same way that the villains of the series have been doing all along! Even Escape only forced her to do ruthless things to mannequins, but this time it's real ghosts that suffer so you can complete the adventure.
Please place Fridge Logic examples on the Headscratchers page.