Q1 : the problem you'll face is that the game does NOT permit theme modding for the time being.
So if you want to mod a theme you'll have to keep its name and effects... But you can change the special theme units (I think) by selecting the monsters and giving them new stats. No new monster can be made usable however. Overall using a theme as a basis for a mod is asking for trouble I suppose ...
Q2 : yes. What happens is that site X is hardcoded to allow recruiting of unit Y - whatever Y is... In my Arco Mod I used the Horse Vale site (normally allowing recruitment of Horse Brothers) to make the sacred Agema Cavalry capitol-only. I just used the HB slots and override them with my cav's stats and graphics.
BTW I'd be gald to help your mod project but have no clue about the background (I mean I've read your Posts but didn't read any of the fiction you're referring to). So I suppose I can only join as a (junior) mod consultant
or tester
!