Several problems here as I see it.
The dealers will tell you the warranty IS in effect using the tuner , however the crossed flags I believe on the tuner (off road use only) may say something different.
The other angle is that they tell you it is not going to effect warranty WITH THEM. If you are on the road and have a break down, the dealer that ends up with the bike may think quite differently. The tuner is a great piece of equipment in the right hands and with a competent tuner and can give you some good results.
My preference is the TFI that requires no dyno time, no dealer time and can be removed without a trace just in case a warranteeable problem pops up. Take a look at the net results of the race tuner verses the TFI and the gains in HP & TQ arrived at between the two , also be fair and compare the total price including installation, setup ( if you don't do it yourself) and dyno time and tell me which one wins. Something to think about with the MOCO looking to get out from under the warranty problems now a days any chance they can get.