> Did Yocto ever clean up how they manage the sysroot?

It's better than before but you still need to sandbox manually if you want good reproducibility.

Honestly, for reproducibility alone. There is better than Yocto nowadays. It is hard to beat Nix at this game. Even Bazel based build flows are somewhat better.

But in the embedded world, Yocto is pretty widespread and almost the de-facto norm for Linux embedded.