Hm, not in my case though...I can not reproduce any of mentioned crew/co2 issues with my modlist/twos and I can stay submerged for 30 to 40 h, depending on crew states used. Once surfaced, the sub is vented and crew is back on the bridge...
But, once again, I always use GUI commands (not key commands) for submerging/surfacing and rarely alttab the game.
@sober
10% in game is more like 1% in real world...