I watched the presentation on the current status of banana linux and saw there were ideas of having unconstrained flatpak apps (bananapak or smth.)
Here is a simpler idea for this, that is more in line with the way of rolling distros. The one that also uses the RedHat stack for this.
Suppose we have a base image that is immutable. Than we can have smth. like /banana-apps/katefor portable apps. It will contain additional files of the app (managed in ostree repo). These apps can have regular arch packages as dependencies (probably with some light adaptation).
Finally, composefs will be in charge of deduplication and using EROFS for storage. This is much simpler than flatpak.