It is difficult for a dealership to price a modded vehicle. The resale becomes much more difficult since the target buying audience has narrowed considerably.
I used to sell Ducatis, MVs, BMWs and Aprilias. We had modded Ducs come in all the time and many of them left in a huff when they could not trade them in at what they thought the bikes were worth.
Personally, I would never buy a modded vehicle. Strong possibility the owner could have beaten the snot out of it. Strong argument for saving all your OEM stuff!