1. “Wheel” signatures (e.g. RECORD.jws) were specified but never actually implemented in any major packaging installer, to the best of my knowledge. In that sense it’s not really meaningful to ask whether they’re “still” supported, since nothing ever did support them unfortunately. The reasons for that are multifaceted, but a single easily identifiable reason is that they don’t solve the key/identity distribution problem.
2. The primary benefit of index-supplied hashing is for lockfiles. Specifically, they make lockfiles like uv.lock and pylock.toml useful/meaningful.
3. Is the source distribution problem, and is sort of fundamental to any packaging system that has any amount of dynamism in it. There’s a good argument to be made for reducing unnecessary dynamism (e.g. via wheels), but a nontrivial percent of Python users actually want this behavior.
Re: files: I think you’re getting confused about distribution files (sdists and wheels) versus the individual contents therein. You can’t modify distribution files on PyPI, you can only add new, unique ones. And this is now restricted to 14 days for each release.