That might have to do with the fact that it is specifically the third auto that restores health. The phantom hit tehnically has no damage of its own and only triggers hit effects, so with Aatrox it might be the fact that since there is no damage, his passive doesnt recognize it while the coding says that it is already past the particular auto that allows it to hit.
To clarify, what I think is happening is:
1st hit- Deals AD damage and procs both the first stack on Aatrox's W and the passive on Sated Devourer, marking Aatrox with an invisible buff that says that his next auto will hit twice, the second for no damage.
2nd hit-Deals AD damage again and gives the second stack on the W passive, and the Phantom Hit occurs almost but a millisecond after the autoattack is confirmed to have landed.
3rd (technically) hit- The Phantom Hit is supposed to be an autoattack with no base damage.
Either the coding says that the scaling for this auto is the champion's ad minus his ad, or it simply makes it so that the damage is technically nonexistent.
Whichever way the coding works, I think that the other side of the W passive, which gives extra damage in exchange for health, is the cause of that bug. Not really sure on the specifics, but I think that's how it's going down in terms of what the game is thinking.