I remember this particular wrinkle driving me batty for ages - It's something that is in MET, but not in the Tabletop. (Or now is in the tabletop with the new God Machine rules revision).
The only thing I've found so far in the code that would help with stuff like that would be the discount eval script that some Vampire Clans and Changeling Kiths get:
This is the Artificer's Blessing one (CtL, Manakin Kith), which makes Artifice go from 6xDot to 5xDot
Code:
perform hero.assign[Discount1.cArtifice]
You could try applying this discount to merits (although that'd take a while), but I think manually adjusting the cost is going to be the only really effective way to do it.