If you want to be historic, use the remove flag part of the mod when you are going from base into international waters. When returning to port (save your game) you restart with the historic flag mod enabled in the JGSME or whatever it is called. You can leave the historic flag mod in the mod list only move the "remove flags" thingie around.
I do it all the time since U boats only flew their fags when entering or leaving port. Never out there....
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