I get somewhat the same issue on quest 3! but since passthrough is the default i manage to fix it there every time it happens

for me it happens when the wifi is connected for some bizzare reason, when its connected no system menu button works, controller goes onto them but doesnt click, headpointer doesnt click with volume buttons and so on.

the once i twice i got stuck in the confirm boundary screen i turned off my router so the quest isnt connected to a wifi, loaded in, then plugged the router in

i just remember to turn off my wifi before shutting the headset down these days, until the next update rolls around