I guess it comes down to who paid for the upgrade - if it was Ford then I wuld assume that they will put the final value up by a percentage of the kit as well as make you pay a little bot more on the monthly payments. If, however, it was you that had it fitted then they, in theory, could tell you to remove it if you are going to hand the car back!!
I don't think they would tell you to remove it but it would probably be silly to hand it back. Equally I don't think they have any obligation to give you more if you hand it back and walk away. If you decided to use it as a trade in at the end of the options deal you would probably get a higher value than the gmfv. If however you are going to keep the car you pay them the gmfv.