I tried to answer myself to the question above, and I think that maybe the Emperor and Traitor should subtract 1 point from the regular damage as if fighting over the breached fortification... Why? Because Emperor (outer palace) fighting forces that are in the plateau suffers no penalty but fighting against Horus in the Inner Palace does suffer 2 pts. The same is with the Traitor: the forces in the Inner Palace suffer no penalty, but the forces fighting from plateau do. Thus - 1 pt of regular damage for both sides.
When Horus and his troops perish in the Inner palace, then the imperial forces stop having any penalty (regardless that the game is over due to Horus' death). In this case the Traitor player has - 2 pts penalty (because he is only in the plateau)
When the Traitor troops fighting from plateau are destroyed, then the Traitor player stops having any penalty. And the imperial forces start having -2 pts penalty.
Are: Inner Palace, Imperial Fists Fortress Monastery and Forbidden Monastery fortified areas in comparison to outer palaces? In other words, do troops standing in outer palaces areas suffer - 2 pts penalty in regular damage when fighting forces stationed in the Inner Palace, Imperial Fists Fortress Monastery and Forbidden Monastery areas?