The first capital was Seleukeia and only in the middle of the 3rd century BC, Antiocheia became the residence of the Basileus iirc...
Although it wasn't unusual for the ruler to take control of the western territories, while his heir ruled the Upper Satrapies (eastern ones)...

Still most of the time, the Basileus was campaigning anyway. As for letting settlements rebel etc, up to how you want to play the game...

Babylonia shrinked a lot in population, in order to settle and develop Seleukeia, and most of all Nikator was successful in the east, because he allowed great autonomy to the babylonian upper classes, gaining favour and consensus. So I'd leave it as type 3, but one can always change history ;)

Mikra Asia, by the time of Antiochos Megas, was pretty "centralized", Zeuxis was nominated satrap of Lydia and made Viceroy of the whole area. I'd guess you could eventually upgrade it to a type 2, but Mazaka was the capital of Kappadokia, its Basileis were pretty much independent, might even be better to set a type 4 and recruit a local ruler...