Logic dictates that adding an armored kilt to an armored coat would have the two stacking their bonuses, as well as their ACP and ASF (the kilt only gives an additional +1 anyway, so it's not even that fantastic). The combination, while still being actually medium armor, would (as described) be considered heavy armor for non-proficiency penalties and speed penalties. Otherwise there'd quite literally be no point in wearing an armored kilt ever.
As for the (at least this is what I felt was implied, feel free to correct me) armor bonuses not stacking for the purpose of the linked description, I feel that's intended to mean that wearing an armored coat with, say, full plate, that the full plate supercedes it entirely, penalties and all, but wearing it over a different kind of medium armor or light armor would let you use the better AC of the two (like an Armored Coat under/over Studded Leather), but also the worse of all the other categories between the two. Looking at the different types of armor, though...I'm failing to see why anyone would ever wear an armored coat with any other kind of armor.
The main benefit of the armored coat is the ease of donning/removing and that it's half the price of a chain shirt. Otherwise you'd just go with the chain shirt.