The fact that I can select files to add/commit with checkboxes and permanently check a box that will push every commit is exactly what I want 99% of the time. I know that isn't the "git way", but the "git way" has no value for the kind of projects I work on.

The "git way" is just whatever way you want. If you want a central server that you always push to, that is fine; there is no problem with that.

The problem is with that particular tooling. That tooling presents a workflow that is perfectly fine (though it is problematic that it does not facilitate alternative workflows, which becomes particularly problematic when working on a team with other users), but it obscures what is actually going on and executes that workflow imperfectly, generally falling over in rather novel ways. When it fucks something up, and it eventually will, you will need an understanding of the basic concepts underlying git to figure out what went wrong. I'm not saying you need to know how to use the default git porcelain, I'm saying you need to be aware of the concepts underlying git.