Have you ever worked with a package manager for a programming language?

In almost every case it is the sole duty of the people using the packages to ensure they adhere to whatever standards they desire. This is how packaging software works in basically every case.

>The package system should also be capable of applying its own patches to packages; if something must break for backwards compatibility, the package system should provide patches to fix the broken packages until the upstreams develops their own fixes.

This is just you not understanding software. This is obviously not possible, it also is not desirable.