It is certainly strange. I don't know the particular year of your boat, but from what I've seen, I don't really see any issues with adding a trolling motor. That boat doesn't seem any different than any other skiff on here. I think I would seek more specific information regarding the reasoning behind their decision. I have a Maverick Pathfinder 1700T and will most certainly be, well in the future, grabbing up an I-Pilot on a 55# Minn Kota.
I would seek another opinion. The I-Pilot itself is simply supplying the unit with a new "brain". Kind of like putting a wireless card in your computer. Plug it in, and it works.
ED: After reading your post again, it would appear to me the particular trolling motor you purchased was considered to be to big? Perhaps the shaft is to long and needed to be cut down by a Minn Kota certified shop? I-Pilot can be purchased for various Minn Kota Trolling motors. That is unless of course, there is some under laying issue with the vessel it's self we are un-aware of.