Yes, it doesn't work out of the box. Proton games literally won't launch. You need to run this command (at least on atomic distros):
flatpak permission-set background background com.valvesoftware.Steam yes
https://github.com/AeonDesktop/Project/wiki/Troubleshooting#steam-flatpak-opens-but-cant-start-games
Mangohud also doesn't work without modifications, as well as a couple games having absolutely abysmal framerates like rocket league.
Gamemode doesn't work AFAIK
It is a worse experience in general, but works for a lot of people.