You made me Look! My 79 CJ, 304, that came with the 3 sp., I replaced with a T-18 from a 78 CJ 6cly. My T-18 has two mounting holes Close together on the drivers side. That "Hole" has a stud in it with a nut holding the tranny. The bottom hole that Your T-18 is bolted to, is Not used on mine. My T-18 doesn't have the bottom hole mount. I guess their different years of T-18, or you got a Ford version. I don't see any reason to close the hole. Bellhousing is not sealed.
The Pirate site shows the holes & were the stud goes.