No way...there isnt a manual trans in a YJ that is supposed to have ATF in it. The Aisin transmissions...AX15 in a 6cyl, and AX5 in a 4cyl, from 90-95 take 75w90 as the choice lube. Some guys run 80w90 because its in the axles, and just easier to keep 1 grade of gear oil on hand.
The T-case runs ATF as well as the autos, but not in the manuals in a YJ.
Maybe in the newer Wranglers, I dont have a lot of knowledge on them. If it says to run ATF in you manual, thats a misprint.