I would say that a gestalt incarnate 2//totemist 2 would have all the class features of a non-gestalt incarnate 2/totemist 2.(But obviously only the skill points, HP, saves and BAB of an ECL 2 character)

Otherwise, you get some wonkiness when dealing with certain features like someone taking rogue//SA fighter and winding up with only +10d6 SA at L20, while a rogue//warblade 1/SA fighter x gets +20d6.