Found a way to use gamescope with Heroic launcher on flatpak.

Instead of putting: gamescope [arguments] in the wrapper section, instead you would do: /usr/lib/extensions/vulkan/gamescope/bin/gamescope [arguments]. You just need the gamescope vulkan layer installed on flatpak.

Might also work with other launchers, but i dont know cause i havent tested. Just thought id share this with anyone else who had this problem like i did.