You might just as well start using SH3Commander.

It will give you the option of selecting year and Uboat-type, within historical limits if you want.
Untill GWX was released, I had never used SH3C, because I always wanted to keep things simple.
Then I was looking for a way to set no-fatigue in GWX, and someone adviced me to give SH3C a go.
So I did, and I never will go back.
Take a look at it's options, in the
readme...maybe it's enough to convince you, even if you can't set it to use a typeXXI in '41? (haven't tried myself).