USD File structure on disk. Nested or not?

Relative (anchored) paths do generally bypass some of the resolving logic, because it leverages the already-resolved path of the layer that contains the reference. But I’d suggest to use them when the referenced file is naturally part of “the same bundle of stuff”. For example, in our pipeline, we publish/version assets mostly monolithically, so all of its USD layers get revved at the same time. (Not entirely true as assets can reference other assets). But to the point you initially had and then removed, if you are relying on the contents of your asset-paths to specify versioning (which is all the ArDefaultResolver provides you with), then agreed it would get gnarly.

Versioning is, I think, a key reason studios implement/customize their own resolver.