Any idea why this shift shaft seal would be leaking?

Removing the pan and valve body is WORK...just do it right. Sure, you might get lucky doing it from the top, but most of us are so slow anyway, that the biggest part of the job is jacking up the car. There could be a problem with the shaft or case that you can't see doing it from the top...I don't like to put stuff together and then have to wonder if it's going to work...If you're going to work on your own transmission; dropping a pan and valve body is no big deal.