I use Fedora Silverblue and I love that my system is exactly the default out of the box distro, with just a couple diffs that are tracked in rom-ostree.
I’ve had frustrations in the past where I install packages to try something, then remove them and forever have something hanging around. Eventually one of those things inevitably breaks an upgrade or dependency resolve.
Installing apps as flatpacks is fine. I don’t love the duplication of system files, but do love that the apps aren’t tied to my distro version.
I also like that all updates happen silently in the background and I just reboot once a week or so. Never think about it.
I feel like the Fedora Atomic distros are great for people who mostly just want a working system and not to tinker endlessly. You can tinker, but it isn’t the default and it’s basically impossible to get into a bad state permanently.
Have you tried rpm-ostree apply-live? https://coreos.github.io/rpm-ostree/apply-live/