I think the Ju88 crews are looking ok in size and they simply feature a different default position in the screenshots. I can sit inside a plane, stretch my legs and place my feet on the pedals. I can also sit inside the same plane and stand with my legs forming a 90 degree angle at the knees, in which case my feet will be resting on the floor and not on the pedals. That doesn't mean i magically became shorter, i'm just sitting in a different position that doesn't allow me to reach the pedals
So, it could be that the Ju88 pilot is animated with his legs in this position (viewed from the left side):
_|-
instead of this position:
_/-