I'll respond here since can't reply to the original comment:
1. "leading stars" -- I think the solution is org-hide-leading-stars (and it is basically the hack you are describing)
2. "now it takes multiple seconds to refresh my agenda view" -- org-super-agenda is a pretty mature library handles groups well. As for performance, the most significant speedup for me was setting org-agenda-span to a lower value
3. "it's actually pretty hard to find good examples of a full org-mode workflow." -- agree. One reason is perhaps because it's quite hard to communicate your workflow to other people becaue it's too specific to your needs.
4. "But problematically I now have a lot of files with similar names" -- yep, refile-outline-path, but also uniquify helps a lot.
5. "Apparently org-mode deliberately prevents the end user from adding their own custom emphasis formats" -- don't know whether that's the case; but you can abuse org-add-link-type, then you could write [highlight:Some text to highligtht], and do whatever styling you want during the export. Hacky, but kinda does the job.
Finally, it's at least possible in theory to override any org-mode function and change the logic. Of course, you can do it with any other text editor, but it would be way less effort to hack Emacs (even if it's dirty and adhoc).
I can however understand the frustration. It took me several attempts to pick up Emacs and Org-mode specifically. And I'm still very often frustrated by it, but I personally find being able to bend your editor into doing exactly what you want worth the effort.