Marigold Girl idolizes Queen Tara and asked her mom if she can be queen when she grows up. She does become the new queen. She's not given a name, but let's look closer: MARIgold Girl or Mary. Remember that in the Bible, Mary was chosen by God to help the world. Queen Tara chose Marigold Girl to continue helping their world.
Tara's choice in a pod represents first-time audience's expectations: Similar to Mub and Grub thinking she'll pick the biggest pod, the audience would think that MK is the next heir. And by exceeding their expectations by choosing a small pod, her choice in the Marigold girl was not the audience's first guess.
Boggans and their forces expressly represent rot and decay, but mushroom characters are heavily implied to be allied with the forest proper. Mushrooms being fungi that feed on decayed matter, they'd logically be Boggan-servants instead.
It's much more likely that the Boggans cause unnaturally fast decay at a rate that would cause complete destruction of the forest, while the "good" decomposers like the mushrooms cause decay at an ecologically-sustainable speed.
On a similar note, decay is actually a vital part of ecology, so portraying it as a force of evil is actually rather ignorant for an environmentalist film.
HEALTHY decay is a vital part of ecology. The level of destruction that Mandrake was aiming for was decay that was at an unnatural speed and rate. There's a balance that the Leafmen were aiming for by keeping it in check. Allowing Mandrake's influence to spread even an inch would have taken umpteenth square miles of forest.
Mushrooms aren't just about decay: many species are symbiotic with trees, extracting minerals that plants can't easily acquire from poor soil and exchanging them for a share of the sugars which trees send down to their roots. It's likely that the forest wouldn't even exist without the help of such fungi.
Crows, bats, and star-nosed moles appear more or less OK with serving Boggans, even though the Boggans are destroying the ecosystem that these animals are a part of. How come there aren't any of them in the living forest? That's where they would rather live in real life.
There most likely are at least neutrally-aligned bats and moles living in the forest, but being more elusive than other forest creatures (bats being active only at night, and moles living almost entirely underground), they don't have much prominence outside their own ecological niches. The crows, on the other hand... Well, they are at least partially carrion eaters, so maybe a large number of them have simply run afoul of the Boggans?
Furthermore, every animal bigger than the Leafmen and Boggans appears to be non-sentient, so those employed by Mandrake probably have no say in the matter.
Grackles, not crows. Look at the tails and listen to the calls.
If the fruit fly had a lifespan of a couple of minutes, how did he have enough time to get into the party and get a drink? Was he born there?