If you're starting early in the war, you might get away with running unattended, but I don't think it's a great idea. Just my opinion. You'd be better off to be sure to only run it when you're in earshot of the sub, so you can hear what the CE and WO say.
In the later years of the war, running as you stated above would very likely be suicidal, as you're very likely to be detected even if you submerge to Periscope Depth. Ad to that that when you automatically dive, you'd be going whatever speed you set your sub to run at. If you only travel at ahead slow, that wouldn't be so bad, except it would take you ages to get anywhere. If you run faster, when you automatically submerge, you'd be making a lot of noise, increasing the chances you'll be detected by any enemy warship that makes you dive.
Anyway, that's my thoughts. Good luck, however you chose to do it.