I just did the transmission fluid complete drain and refill this past weekend, its lifted probably 3.5" front 2.5" rear didn't even think about the fluid check level since its lifted. Wife has not had any problems thus far and I really don't feel I will have any. I made sure to put a little extra fluid in the transmission so that when I got the AT-Temp light to come on and I unbolted the level check bolt that some would come out so I didn't have to shut down, add and restart.
There's an acceptable range around the spec, consensus on here is that lifted/leveled within reason is fine to check level as manual says (level ground too). Now if you really want to be a stickler you could jack up or block up whatever end you need to get the pan perfectly level but shouldn't matter.