Here
http://www.uboat.net/men/crew/commander.htm (bottom of page)
is a link to the last(highest) rank of all uboat commanders. Six commanders never reached higher than leutnant zS so those did obviously start out their command as leutnants. 625 commanders never made it past oberleutnant zS. Probably some of those 625 started their uboat commanding as leutnants too.
But I agree with your point that if you start early in the war you should start with higher rank than Leutnant z.S.