These systems were designed for a hierarchical filesystem so it is natural that that is what they support. I'm sure that if tag-based filesystems were the default they would have an equally suitable design that worked well there. This could be as simple as specifying the "project" as a set of tags. For example project=camera and maybe compile a submodule with project=camera,module=ui. Then the files inside could be processed by the build tool.

Of course for any tag-based filesystem to take over it will probably need a compatibility mode. I can imagine something simple as a path=myproj/src/main.rs.