i think i still had audio issues, was on a gaming binge from noon till now, i updated just before i started playing too, but saw that the newest update includes a new scheduler. I was playing RE and had a bit of sound crackling still
User (as it implies) is a flatpak installed to the user, so only that specific user can use it. System is system-wide. Usually there's no difference between them except for that.
And just to be clear, using one over the other will never cause issues. Some apps prefer to be installed as system (I believe GPU Screen Recorder used to do this) but it's just the case of uninstalling it as user and re-installing as system.
In this case I'm installing Retrodeck, and I am more concerned about the fact that maybe there are some hardcoded locations that need to be on the "deck" user folder and things like that