I find the 12 very puzzling as well. In the example, a 3RP trait is replaced with a 2RP trait. So I saw three possibilities:
A) No change, costs are static
B) Recalculate. In this case -3 +2 for a change of minus 1
C) Add new trait cost as a kind of "customization tax" for a change of plus 2
I'm very curious how a plus 1 would be achieved in this case.