In an interesting case of timing, I read an article a few days ago complaining about (among other things) the fact that Flatpak's aren't always isolated and it's not always obvious at first glance whether they are...

...and later that day I was reading about the Minecraft Fracturizer malware that tries to infect every .jar on your system, and at least one launcher's Flatpak was isolated enough that it could only infect the temporary filesystem used to run the game.