Jeff,
In this case it was really 2 different castings, as the hydro and gear drive transaxles are very different from the pinion gear forward. However, your point rings true in that just because the back 1/2 of the casting is the same, it doesn't have to be machined the same. In fact, the indention in the casting probably was there specifically to save tooling wear...why drill it all the way through, when you can cast it 3/4 of the way through!