Change the crate version rate limit from being per-user to per-crate

[epage]

This is being split off of rust-lang/cargo#13530 so there is a place to follow discussions on this topic.

From rust-lang/cargo#13530

For new version publishing, the current restriction is per user, which is why we encounter issues with workspace publishing failures. crates.io might consider changing the restriction from per user to per crate for new versions. This should solve most of the problems.