Yeah, it’s linked to the independence thing.
It’s also linked to how right now, bulk actions behave a bit inconsistently. For commands like bold (Ctrl+B), children items on all levels are affected. For some other commands, like unchecking mentioned by @Dave, only affect top level items. If we make everything consistent, it would at least solve his problem.
The issue is that for some commands, it makes more sense to only affect the first category. Inconsistency sucks though.