Sounds like you got screwed.

If the dealership is sophisticated enough to know about Mobil 1 color variations, they should be equally knowledgeable on resetting your FSS.

If it were mine and I planned on keeping it for a long time, I'd go to an independant and get it done correctly - fleece filter and 8 1/2 quarts of M1 0W-40.

You can check Mobil 1's website for the official word on the color darkening, but I think you're being lied to by the dealer.