In that context, having all packages be “system-wide” made sense. All the virtual env shenanigans won’t ever fix that.

Sorry, but you'll need to explain this a little bit more to me. That's precisely what virtual env shenanigans do - make it so that your environment isn't referencing the system-wide packages. I can totally see that it's a problem if your virtual env tooling fails to work as expected and you can't activate your environment (FWIW, simply old python -m venv venv; source venv/bin/activate has never let me down in ~10 years of professional programming, but I do believe you when you say that Poetry and Conda have broken on you); but assuming that the tools work, the problem you've described completely goes away.