Like @Forpli alredy wrotes: These are only Runtimes for the Programs, not the entire Gnome Shell.
But You have a Point with ''diffferent Versions'' here. It can be that a Flatpak uses Gnome 49 and another Gnome 48 as Runtime. Then both will be installed.
But when several Flatpaks are using the same Dependency. This will be only downloaded once and then will be shared.