You are quite right of course, no reason the stronghold can't be any and all of those things or, better yet, put to a vote on the forums? The more freedom we have to define the stronghold by our choices and actions from the start of the game and throughout, the better, in my opinion.
I don't know about you, but in a number of games I would like to have been more involved in various factions. Not just walking in one day and suddenly finding myself at the top with no where else to go from there, but having that allegiance play a part for the rest of the story through some re-activity I don't think that'll be a problem for this game though