What you say sound logical, in practice animators are used to work on a shot basis.
I’ve seen productions where all the lipsync was done in a separated pass as one animation, then imported in each shot. Generally animators import animation from previous shot to start as a basis.
It depends on the animation style. I’ve made a breakdow of my last project , you can see that animation and layout can be quite different from one shot to the other : Boon & Pimento : Cartoon series made with blender - #31 by sozap
I think it would be better for your pipeline to support both ways of doing, what you suggest is also interesting to have !
Anyway, that’s really cool ! It’s great to think about having a good folder structure. In the end it’s never perfect but you can always improve on the next project.
What I found difficult to manage is props, you can have hundred of them , having them all in the same folder is unpractical, making sub-category is also tricky sometime. But in the end even if that’s not perfect it still work.