If package management was as a happily solved of a problem as you imply, I think we would see fewer solutions out there. Each tends to solve for the needs of its own environment, users, and sometimes the whims and bias of its developers. When you ask, why not use "gems or maven jars or cpan or whatever" I think you have to stop and ask, "why are there so many options already?"

There are many views out there for what the answer should be for Chef cookbook workflow. What you are "baffled" by, another person uses daily and argues for.

When using knife to download a cookbook into your git managed chef repository, it creates a 'vendor' branch to store the upstream version. You can utilize this to create diffs and patches to contribute back to that cookbook project. It is up to the author exactly how to do that.

Some really like git submodules, others prefer one cookbook per git repository, some just have one company-wide repository and ask you to fork and apply branches against.

I think you're right about the 'Chef toolchain.' There are [large enterprise] users of Chef who don't care that Chef is written in Ruby nor particularly want to learn Ruby. They want to use Chef. Opscode continues to strive to provide tools to make the workflow easier for Chef users as a whole over preference to a particular toolchain, especially one tied to and solving problems for a single language.