Although you could calculate the area of the throttle rod and thickness of the throttle plate and subtract it from the area of 90mm of throttle body, I think it would be math for the sake of math and get you poor results.
My reasoning is that you would end up slightly smaller than 90mm and then have a turbulent area where the TB met the EGR plate.
If it were me, I would blend the plate to whatever is in front and behind it, and it that's a 90 mm TB, that's what I would machine it to.
Now you could get fancy and try to dimple the short side after machining if you are trying to slow air around a corner, etc, but hard to do that stuff without a flow bench and I have to tell you, even HARDER to find a 1000+ cfm flow bench. I tried to when I did my MAF work and never got there, so ultimately had to go TLAR. (That looks about right)