Agree. This puts a spanner in the works.
I read through most of your suggested workflow, which seems to make sense. In my opinion some kind of similar hierachical structure within Nuendo might be helpful but, of course, it remains to be seen how such a structure could be succesfully implemented. Where would it live within Nuendo? Do you see it as an extension to Media Bay?
Some might say we already have some of this within Media Bay and also if a project is organised logically and uses multiple marker tracks and other functions. IMO it would still be better to work in one large project for ease of access to all sounds.
It might also be valuable to know how you can get closer to your requirements using the functions Nuendo already has.