1. When I first learned about the alternatives system, I initially assumed that it was in use for every single binary - that there was an alternatives selection to decide what provided /bin/ls, and one to choose /bin/sh, and one to determinue /bin/chmod, etc. (I mean, /bin/sh sometimes is depending on your distro and how they feel about bash/dash/ash but you get the idea.) And honestly I still kinda feel like that's a good idea, though it leans toward redoing how packages work in a way that reminds me of nix and Gobo; /bin becomes just a symlink farm pointing into per-package bin directories.
2. Although this kind of bulk-replacement is a good initial test, I feel like letting packages directly depend on GNU coreutils or not is maybe a good way to go - you can test packages one by one and switch them to point to a virtual package as they're validated, thereby letting the package manager properly manage dependencies by giving it enough information to asses the situation.