In an ideal world a flatpak could register the cli commands it wants to present to the user, and some alternatives system could manage which flatpak gets which command if there were collisions.

This has been my dream ever since I discovered Flatpak. I wish it becomes the case one day.

It's good that there has been partial progress in that direction. Let me give an example with the Floorp browser. I can do a flatpak install floorp and I can do a killall floorp and they will work. If we can somehow get a way of accessing flatpaks as if they're regular packages via the terminal (is it possible to build a program to do this and have it packaged as a flatpak?; Maybe a program that creates a oneliner script to act as an "alias" in a directory (within $HOME so it works on immutable systems) that gets added to $PATH), that would be amazing!