Lutris

[modest cliff]

better to install it as system package, or flatpak?

[brave arch]

System.

Flatpak by design bypasses your password and can mess around in your root directories. Its only supposed to edit /var/lib/flatpak/, however if there is a security venerability, it is there. You can stop this using a polkit file.

As far as better or not, it largely depends on what you are installing. Flatpak sandboxes, which means if its something like discord, you can only drag and drop from ~/Photos And ~/Downloads, because that is all discord can see. Things like steam can be a little broken, and you cannot make .desktop shortcuts for games.

It really depends on what you are trying to install, but if its a program you trust, or need full functionality out of, use apt and install it natively.