Most of the time dealers have no idea whats been done to a car, mainly because the person trading it in doesn't hand over maint. papers or the dealer scraps the paperwork after trade-in. But mainly because the dealerships aren't gearheads or turn-wrenches, therefore when the see a mustang with all the factory looking body panels they just assume "Stock"
My friend bought an 04 GT with a super, modded headers and exhaust, a full tune with the married tuner being found in the trunk under the spare, and about 1-2k in other mods not including labor. the dealership thought it was pretty stock (even after the mechanics took a look at it) and sold it for 5k because the bumpers were all chipped and there was some broken interior bezels.
I was looking at a de-badged cobra listed as a GT and at a GT price, but it had been in a fender bender so the guy had replaced the front and rear bumpers with a GT's (or he just made it a sleeper/pride hurter with a story to make up for his crappy decision :sorry)
*EDIT*
When I used to work at a Nissan dealership, they bought a 350z with full nitrous and twins, lambo doors, and a crappy suspension setup because the GM "thought it looked good" :/