I was under the impression that using os-tree should be totally avoided for anything other than necessary system programs

Interaction with ostree directly shouldn't occur that often; with sudo ostree admin pin *number* (and its -u option) probably being the commands your average Joe should interact with. You probably meant rpm-ostree.

and all other software should be installed with flatpaks or containers.

It's indeed true that initially Fedora intended flatpaks should be preferred. If the software isn't available there, then Toolbx(/Distrobox) is used to access it through a container. And if all else fails, then it's layered through the rpm-ostree command.

I now understand that using os-tree for some programs is inevitable, and I should embrace it, though still catiously to maintain as clean of an OS as possible for maximum longevity.

You're getting the drill! Though, I wonder why you weren't able to rebase to uBlue and had to resort to installing the Nvidia drivers through RPM Fusion instead. It's fine as long as it works, but I imagine that some issues might arise eventually. So consider sharing the steps you took so that the community might help out; perhaps even over at uBlue Discord. You could also just share it here if you will.