i bet your towers are not standing straight (vertical) or
your bed is not clearly horizontal
i've recreated your picture with some assumptions (for example that your SW calculates properly and your steppers and motors act well)
take a look here

if you deliver your printer dimensions
- tower height (from the base)
- tower distance from the center
- bed distance (height) from the base
i can calculate what is inclination angle on all towers but i suppose it's not really important
the important thing is to set them straight ;)
we can see from the picture that towerA is the most inclined to the center or
the bed highest point is next to towerA
(and i bet one of those or both cause the issue)
EDIT
i've made some calculations based on imagined assuptions of the tower height
here are details
towerH | inclination
-----------+----------------
300mm | 0.11deg
400mm | 0.08deg
500mm | 0.06deg
seems to be quite small but in fact your differences in dimensions are also small
inclination of towerB is bigger as there is bigger difference in dimensions
so maybe the issue is more in bed "horizontality"
would be good if you would check and measure these params
EDIT2
here goes the explanation why bed inclination causes dimension distortion

of course it's exaggerated but it's just to show the issue