Sounds like you've got their number. I doubt they will even have to touch your CC install in order to attach the supplemental harness. I would definitely look for another dealer.
Unfortunately, all of the other dealerships are pretty far away. Ride Now has a near monopoly on Yamaha dealerships around Phoenix.
I called Yamaha, and while they would not commit to covering the extra work without having an estimate on it from the dealer, I was told that they would not have a problem covering any extra labor due to the servo location. I have the product specialist's direct phone number to give to the dealer to call when/if they get to the point where they would need to R/R the Cruise servo.
I also want to point out that the Yamaha reps to whom I spoke were very courteous, understanding and helpful. I was kind of surprised I didn't even get a lecture on the dangers of adding non-OEM modifications.
So I'll probably take the bike back to the same dealer this afternoon and hope for the best. I guess if it ends up costing me $100 or so do get the work done, it's probably still worth it to know the problem has been addressed.
I also should probably mention that the only work I've actually had done at this dealership before was other recall work on the FJR, and that process went very smoothly. Other times I have considered having them do service on my bikes, but their estimates always scared me off.