I’ve never adjusted the screen using the Display:0 thing.

If you have a spare SD Card, I’d recommend building up a “clean” OS for testing, to see if something was done that unintentionally broke the rotate feature.

That’s one of the first things I do when I’m having trouble with something I’m trying to do - I build a new OS, install the basics, and test with it, in this case using https://pimylifeup.com/raspberry-pi-rotate-screen/ as a guide.

Just to confirm as you’ve mentioned multiple Pi versions -

You’ve not shared SD cards between them, right?
You haven’t copied the rotate config files from one to the other, right?

Whichever unit is gonna be used in your final product, keep everything on that, and in the future, report to us which hardware and OS you’re using for bug control, as things have changed dramatically over the years. 🙂