Last I checked, for the 4T60-E's there were 6 versions.
1991-1993 CHEVY (3.1, 3.4 DOHC)
1991-1993 CADDY (4.5 and 4.9)
1991-1993 BUICK (3800)
1994-1997 CHEVY (3100, 3.4 DOCH til 1996, the 1997 DOHC was a 4T65-E)
1994-1996 CADDY (4.9 I think 1996 was the last year you could get a 4.9 in a caddy before being replaced with the 4.6 Northstar. If they had a 1997 4.9, I don't know what transmission it would have had)
1994-1996 or 1997 BUICK (3800).
There is also a RARE 1993 Cutlass Supreme with a 3100. I am not sure which Version of the Transmission it got, but It was most likely the 1994-1997 CHEVY one.
Differences are internal. the QDM's in the ECM/PCM that controls them are different between the 3 engine brands, so when trying to interchange.
If you want PLUG N PLAY, you need specifics, otherwise, you have to crack open the sides, and swap out the valve bodies, and wiring.
Not sure if people have found ways around them. My information is several years out of date from my foray into Lincoln Land.