Transforming mutations into react-compatible object creation is not always trivial, particularly with twisty object graphs. I once spent a week trying to untangle a reducer monstrosity that wished it could mutate. In the end, I don't think I totally fixed it. It can be hard.
Joking aside, you're right, often it's almost easier in recursive cases to just go with flat object lists and keeping identities on objects and keep parent id's around.
In my view, React is a theoretically beautiful piece of software, and if you're planning on building a synchronized networked system keeping in line with what makes it beautiful will give you it almost for free.
For many practical cases (especially smaller SPA's/pages) however it's probably better to just go with Vue or similar and mutate away and let the system handle all update checks for you instead.
