For something like Tailscale, running as a Flatpak would require the user to relax the sanbox boundaries, assuming it would work at all!
It's probably easier to script up the installation via package manager. You also get the benefit of upgrades along with the rest of the system.
Furthermore, I haven't seen a single instance of Flatpak being used to install applications on headless servers.
I also don't know many sysadmins who would be happy that each application they install in their servers will come with a full set of dependencies rather than being dynamically linked to the base system.
It's probably easier to script up the installation via package manager. You also get the benefit of upgrades along with the rest of the system.
Furthermore, I haven't seen a single instance of Flatpak being used to install applications on headless servers.
I also don't know many sysadmins who would be happy that each application they install in their servers will come with a full set of dependencies rather than being dynamically linked to the base system.