Can't speak to your specific box's comings and goings, however,
(a) there is no reason why the third segment has to be constant, while acknowledging that this makes the crew interaction a lot simpler and is fairly standard both for that reason and ops engineering simplicity.
(b) if the critical obstacle is third/fourth segment, there may be a minor advantage in the calculations to maximise RTOW by playing with the third segment height, depending on the specific geometry for the numbers of the day.
(c) any parameter in the AFM calculations which affects altimeter/tapeline deltas may show up as a small variation depending on how the model is set up in the computer, keeping in mind that the height output is what the pilot is looking for on the gauge/tape/whatever.
Old Smokey is a 777 man so he might wade in with some specifics in due course for you ...