base VS vauxite

Like you mentioned, rpm-ostree is meant to be a fallback after non-working options like, in order, flatpak then distrobox/toolbox. But that doesn't mean it can't be used. Keep in mind this is simply a rule of thumb to increase security, stability and rpm-ostree performace, but it's still just a rule of thumb. Silverblue is very flexiible, and I have roughly 600 overlays and while rpm-ostree is slow, the only thing I really do with it is upgrade those packages installed with it, now that my system has the packages I need. Since this can be done automatically (See "man rpm-ostreed.conf") and the system is immutable, the only intervention required is rebooting when necessary (Such as if there's a fixed vulnerability or a new feature update you want). The other nice thing about auto-updates and immutability is that Silverblue is more resistant to breaking while running do to an update of an important system library or the like, since the library isn't even "visible" until the next boot, when those things it depends on are all already setup to use the new version. I also recommend checking out Jorge's flatpak automatic update systemd .timer and .service filese over at https://github.com/ublue-os/base/tree/main/usr/lib/systemd/system and downloading them and using sudo (From a Silverblue terminal) to put them into /etc//systemd/system, doing a "sudo systemctl daemon-reload" and "sudo sytemctl enable flatpak-system-update.timer" . This will update your flatpaks for you. In my opinion, between rpm-ostree auto-updates flatpak updates, you'll have a much smoother experience.

You'll see that the base image installs flatpaks as a post-install step. I really tried to work around this limitation, but haven't been able to via the OCI approach.

It is a Fedora OSTree (IOT, Kinoite, Silverblue, etc.) image customized for specific needs or wants, in this case, XFCE!

To control which flatpaks are installed, I think you need to use the more complicated ostree build tooling. See the Vauxite repo as an example of that approach.