You are right - the transmission and transfer case are two completely separate components. They do not share any fluid and are sealed separately. Gasket maker between them is pointless.
As the poster above said. You would not have caused a transmission leak by doing SYE with the TC still connected to the transmission.
1994 YJ Wrangler, 4.0, AX15, NP231, 35x12.50x15 BFG KM2s, 4" RC lift, 1" lift Boom Shackles, 1" BL, 4.10 gears, 8.8 LSD in rear and D30 Aussie Locker in front, on-board air conversion, Ramsey RE8000 winch.