I would think since we only have a drain hole for filling and chacking the tranny fluid you would need to worry about keeping the tranny at the correct angle so that it would continue to hold the proper amount of fluid and continue to lubricate all the parts properly. If the tranny gets at an angle from improper lift the part of the tranny fluid resouvoir would have fluid at a higher level which would not be a problem but on the other end the higher end of the res would have a lower fluid level possibly causing inproper lube and tranny failure.
If the suspension was untouched, would the way the fluid sits be the same compared to checking it with the tires on the ground vs. a shop checking it while it was on a lift at a shop? Would that change if the front end height was modified?