I get what your saying, but it's just a matter of finding the right workflow.

I'm very much like you infact, so I ended up resorting to just using an Arch Distrobox for pretty much everything. I leave rpm-ostree and Flatpaks alone as far as possible, so I only really have to worry about my Arch for updates and everything else takes care of itself.

You may ask then why not just use Arch? Well of course you can, but I like the idea of having a rock solid base where I know for a fact that I can let it happily update without breaking something. Arch still requires manual intervention every now and then (such as package migrations or some dependency conflicts). Not a big deal if you keep up with the Arch News and Discord announcements etc, but sometimes IRL gets in the way and I'm not up-to-speed with what's happening. With my Bazzite+Arch setup, I'm not super bothered with this, plus it's easy to blow my whole container and set it up again, and in fact I've got a bash script to do just that on one of my other PCs that I don't use regularly (because Arch needs to be updated regularly, otherwise you're in for a nasty surprise when you find out your keyring is out-of-date and pacman has been upgraded and nothing works... with a container, just blow it up and fetch the latest version, reinstall your packages and you're up and running in no time).