1- Starting territories will be unchanged, for the most part. New factions won't make other factions loose territory, since the factions in EB1 are only given what they controlled historically, not what other (new) factions controlled, those are entirely rebel in EB1. And most of the new or removed territories will come and go to regions in 'rebel' hands in EB1.

There may be some unrelated changes. For example, Sophene might have been in the hands of the Hai at the start date and not a Seleukid dependant.

2- The one color per faction will remain. There are many different shades possible, though. And some factions might have similar colors but are on opposite sides of the map, so it won't really matter. (example: The Romani and the Saka nealry have the same color in EB1, but it rarely matters.)