It is due to the "region advantage" in the unit_prod file, same as any military unit as you said. It's not really "undocumented", it just so happens that only one unit can be displayed in the "This region is famous for..." entry on the region parchment. So if two units have a valour bonus in the province, only the one which is higher in the prod-file will show, which for Syria is Nizaris (IIRC). If you don't want v2 assassins rolling around the map, then you can remove the ID_Syria from that column in the unit_prod and Syrian assassins will be indistinguishable from any others. You can't disable a building from a province in MTW unfortunately (it would make modding SO much easier if you could ), the only way to make buildings at all "geographical" is with coastline (ie dependent upon a port) or with resources - so they can only be built where the resource exists.

I'm sure the developers' intention was to recreate or portray the assassin sect of Alamut.