Huh, looking more into it seems 3.33 uses "Gendoh" but 1.11 and 2.22 both use "Gendou". Odd discrepancy I never noticed before.
The English release of 3.33 was pretty bizarre as it was, maybe that has something to do with it.
EDIT: Huh, for a point of comparison it seems the English version of Super Robot Wars V goes for "Gendo" even though its specifically adapting the Rebuild plot with its Eva stages.
"[Cinema] is a labyrinth with a treacherous resemblance to reality." - Andrew Sarris