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Bazzite theorically auto updates but Im not sure it does for me, so I just start the system updater that updates, system, flatpaks, brew etc from time to time when I plan to reboot anyway.
Thanks
Bazzite has GearLever built in for this.
Also, I think they update using topgrade, which doesn't support gearlever afaik. I always manually have to update in gearlever.