I believe the flange for the driveshaft changed from 4-bolt to 3-bolt if I remember correctly - someone else can chime in. But that would just require you to swap out your flange.
Remove S550 3 bolt flange from trans, install the S197 4 bolt flange on the S500 trans and boom. The only difference between S197 and S550 MT82's is the flange and shifter assembly.
3 is a better design for distribution of forces. Think of a 4 legged chair on an uneven floor. Now take a 3 legged chair and sit in it... it won't rock at all. Sure the load potentially goes up 33% per bolt but when stresses are put through it, it will divide it evenly between the 3.
Of course 4 will be inheritly stronger in a brute sense.
The more I think about it I have a feeling it was an engineering and bean counter appeasement move. Better balance as the new coyotes and voodoo spin even faster. And it might be a NVH move too to clean up some of the drivetrain thunks. The bean counters get to keep a 20 cent Bolt so they are happy. Does the GT-350 use the same 3 Bolt setup as a GT in the S550s. Then are the bolts from the 4 lug S197 the same as the ones in the S550 or might the new ones be different, especially larger ?