A car dealer looking to take in a trade, is not "most people". Most people (and even dealers for that matter) will be more than happy to take in a modified mustang, provided the mods are tasteful and reversible. What most aren't willing to do however is give many owners their inflated asking price for those additional mods when the time comes. Mods really add next no additional value to the trade in and depending on what mod it is, may actually get you less.....but try to convince the guy who just spent $5K on mods over the last couple of years that they aren't worth anything when he wants to deal his ride in.
The right mods on the other hand will be appreciated by those who know Mustang....but generally that's strictly private sale territory.
Case in point....you'd be hard pressed today to find a Fox body, or for that matter, even an SN95 Mustang GT that hasn't had some form of modification performed to it at some point. People are still lining up to buy them though.
.....and again, your statement (as far as dealerships are concerned) applies to any Mustang, not GT's exclusively.