hi Capt Cliff, i've thought about your posts for a few days now. i'm writing from an Allies-only POV.
1st, under the orig & patch AE, AmphTF capacity was calculated according to TranTF capacities, inevitably causing probs. one had to mentally/scratch-paperly add the 20% Amph-load penalty to the TF.
2nd, even under the recent betas, AmphTF load is not able to calculate the exact/precise supply req'ment. one must still design the AmphTF w/ greater troop/cargo capacity than req'd, ideally you need to see at least 20% overage in both troop & cargo cap when you hit the Verify Load button.
3rd, IMO this prob is 'in the nature of the game', that is, it takes a lot of game-experience & savvy to load a mongo AmphTF. you can't depend on the screens to tell you true.
4th, IJ Amph loads might seem more accurate, but the IJ is much more willing to load troops into cargo-space.
5th, it's a mistake to load to an undocked AmphTF, loading will be slow & will neglect heavy devices.