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.
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.
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.