This is wrong.
Discover is basically designed to mimic the Software Center in Gnome… it isn’t a bad idea, but it relies on pkgkit which is a compromise - this was rejected by Arch.
Pamac GUI manages Flatpaks, so Discover isn’t required for a GUI.
Also, it is fairly easy to manage flatpaks using the terminal, it is good at searching for software (unlike Pamac GUI sadly) so overall for flatpaks, konsole is your friend.
You didn’t really mention WHICH flatpak you’re interested in, so it’s hard to help… we don’t really know what you want to do.
Your stated aim ‘to make them compatible’ is a very lofty aim, you need to take control of the KDE Plasma development team, as well as the Arch devs, and tell them to change their philosophies.
Manjaro is piggy in the middle, so no chance there…
However, going the Arch way, it’s best to use specific tools for specific jobs. Software is best searched via your browser if you wish to include more options - given that pamac can’t search as well as the flatpak terminal search…
Try it, open your ‘add/remove’ GUI, and type in ‘plexhtpc’.
Then open Konsole (Ctrl_Alt_T) and type flatpak install plexhtpc.
When you update, you can create your own script or alias… but generally many people wouldn’t argue too much with the following:
sudo flatpak -Syu && pamac upgrade && flatpak upgrade
Another issue with Discover would be that it would try to run your upgrades, but it would likely suppress some very important messages in the process.
We don’t like Discover much 
my opinion is that it encourages mindless ‘browse and click to install whatever software looks pretty’…