Do you specific issues with uv that makes you distrust the implementation? Otherwise that reasoning is pretty weird - it's possible to write good software, even when the existing options aren't good. Why would we ask them to limit themselves to what might make sense for worse code?
You're missing the point. No normal user program can ever do what a filesystem can do: deduplicate in a way that is hidden for the user of the filesystem. Unless you want to change everything into a black box managed by the package manager, making everything confusing for users and also maintainers.