The 12.7mm in the tail of the IL2 doesn't save it much, does it?
The 2x 50cal in the Boston doesn't save it much, does it?
The 1xMG131 instead of 2xMG17 wouldn't make too much of an impact (only 33% more power in that one position, maybe slight increase in efficiency not having to jump from left to right gun) isn't going to make it a super killer.
IMO I like the 2xMG17 setup because it's more interesting, and looks a lot more like JU88s I mentally picture when I hear the name Junkers.