It can, but because the Flatpak system depends on APIs like D-Bus getting those to work in headless environments (SSH, framebuffer console, raw TTY) is a pain.

It can, but because the Flatpak system depends on APIs like D-Bus getting those to work in headless environments (SSH, framebuffer console, raw TTY) is a pain. Flatpak will even helpfully link binaries you install to a directory you can add to your $PATH to make command line invocation easy.