Dude, it's offset and crooked. When you bolt the engine to its mounting location, the tranny aligns by default. Crank them down, and you are rocking and rolling. You start phucking with alignment, and you'll screw up driveline phase.
Myself, I think that position is a factory defect, and Pontaic is pissing on your leg and telling you it's raining.
Way back when some of the fgf advisors were even able to think about driving a car, let alone drive one, the 'excuse' for the position was to offset engine torque.
Whether or not my guess is correct, I'll give Pontiac credit for the possible cover up. All you have to do is simply look at the crooked, offset install, and it's a good defense to claim it offsets engine torque.
As for that pos tranny you want to install, I can only guess that it makes no difference in driveline phase. Then again, maybe it would because as you alter the length of the engine/tranny, I see how it could bleed out on driveline phase.
The only tranny I would use is the more-than-well-documented high performanc tranny, the th350 because there isn't another tranny what even comes close. So I have to pretend. That's okay because lots of people around here pretend, and I should also be allowed to pretend.
If I were going to install that pos tranny, something that I have to pretend I'm doing, I would install it according to the natural registere of the engine mounts, and capture the rear location on the relocated crossmember.