Well I found this listing for a qa36/qa42 gearbox with some pictures. Listing seems to be gone but the photos remain, and it appears that the lower plug is the original plug.
https://picclick.com/Cub-Cadet-QA36-...550052215.html
I'll embed the photo too incase the link above goes down.
Anyway, I'd guess that the previous owner of my tractor added another port to simply make filling it with new grease easier? Open both ports, fill form the top until fluid drains from the lower. Figured I'd post the findings here incase anyone else was looking into something similar.