Well, Flatpak always builds the aliases, so as long as the <installation>/exports/bin folder is in $PATH there's no need to symlink.
If you're talking specifically about having symlinks with some arbitrary name that you prefer, then that's something you'll have to do yourself, the Flatpak applications only provide their canonical name after all.
You could probably do something like that with inotify and a simple script though, just point it at the exports/bin folders for the installations that you care about, and set up your own mapping between canonical names and whatever names you prefer.