The 6L80 has 32 splines.
The 6L90 has 34 splines.
It appears as though the 2WD and 4WD trannies are similar in structure. The difference is in the tailhousing adapter; 2WD gets slip yoke while 4WD gets transfer case adapter.
Additionally, on the 4WD trannies, the bolt pattern is the 6-bolt, round GM pattern. This means any transfer case with this pattern should bolt-up with no modifications!
Also, Atlas makes 2 & 4 speed transfer cases with this bolt pattern AND both 32 & 34 spline input shafts. Nice!