In an ideal world, the game would pick the dynasty CoA for the family member with the highest title, and keep the "territorial" CoAs for all the other family members.
That way King Aerys of the Iron Throne has the Targaryen CoA, while Prince Rhaegar has the normal Dragonstone CoA.
Same with Joffrey (Lannister CoA) and Tywin (Westerlands CoA) at the WOT5K start, or Renly (Baratheon CoA) and Stannis (Dragonstone CoA)
And of course the realm naming after dynasties would be disabled...
Don't get me wrong, I like the territorial CoAs created for this mod, but I like the dynasty CoAs better.