If Flatpak wasn't designed or intended for services, I fail to see how it can be recommended as a relevant tool. I get what you're saying about containerization, but Flatpak is as much of a 'solution' to package management as a cork in a bullet wound.
CoreOS (not specifically Fedora CoreOS) used to do that with Docker. I believe the OS ran your standard systemd services and all through interconnected containers. As far as I can tell, the project has been abandoned, though.
I don't think Flatpak is the right tool for the job, it's clearly optimized for UI tools and the occasional command line invocation. Snap may be better for composing a working systems, though that comes with the obvious Snap downsides. Systemd has some great tools to accomplish image/container based operating systems, though I'm not sure how common it's used.
