Also, flatpak has a lot of problems in my opinion, not the least of which is that it has no mechanism for installing to a different disk without creating an entirely new "installation", which in its terminology means a completely new dependency chain too.
The "portals" idea is a pretty good one though, on the whole.
I hear you on installing to different disks, though. Appimages are also an option, but I've found they have a tendency to not actually work between different distros and system versions.
One thing that would be interesting would be to use flatpak "runtimes" to provide a target base system for AppImages, but I don't think that level of cooperation is actually possible within the Linux community.
I don't really think it's an issue though, if you really want portability you shouldn't rely on any software provided by the distribution unless you want to depend on that specific distro.
Flatpak runtimes are basically interchangeable base systems, it seems silly to commit to any one in particular when you can use any number in parallel.
Flatpak has you covered, or at least, it's getting there pretty fast. You'll still need to manage debs for base system stuff but you can install most gui apps as flatpaks now.