For what it's worth, I agree with you about branches, and there are various ongoing discussions about how to make working with branches more convenient. I use an experimental feature called "advance branches" that makes it mostly fit my workflows, and the other benefits of jj are sufficient that I haven't switched back to git.

I create log files of runs, temporary helper scripts, build output, etc. in my working copy all the time.

The solution to this is to just have a more aggressive .gitignore. But also, note that the "working copy commit" isn't generally something you want to push or keep; think of it more like a combination of the git staging index and an automatic stash.