In reply to just some thoughts...

I honestly don't see why it's more efficient to bundle them. I don't see what the gain is. Multiple plugins treated as one entity implies something that should maybe just be in one plugin from the beginning IMO. Uploads should also never be in a Git repository, just as 3rd party software shouldn't either. It means that every time something gets uploaded or updated, you have to commit it to version control. That seems very wrong to me and I don't see how it can be more efficient. Version control is not a backup tool - maybe for the codebase, yes -, but not for stuff like uploads etc. That should be kept somewhere else.

What I mean by "that's the way WordPress works" is that WordPress treats themes and plugins as their own respective entities.

I agree with your last point very much, but I think it is also important to discuss these things - even if we don't agree! Especially in the WordPress community. Even though WordPress has a huge market share and is doing very well, there are still a lot of things WordPress developers are missing out on because parts of the WordPress eco-system is not completely up-to-date with what's going on in the rest of the PHP world (hint: Composer).