Is there something about the nature of Quaal's Feather tokens and the trees they produce magically interacting with wand magic in a weird way that you're going for or there some other significance to how much trouble they seem to have removing or otherwise

Neither. Wanded magic is actually fantastic at dealing with practical problems (see: Molly cooking and cleaning with magic. You could do that with D&D magic, but preparing those spells would often be a liability, as it comes at the cost of more combat-oriented spells.)

No, the trees are still there largely because it’s funnier that way. I think I mentioned in book 1 somewhere, also, that Professor Sprout chose to preserve the tree in Hogwarts because of what a magnificent specimen it was.