I'm not sure that modifications make a car worth less per se. If they use commercial parts and can be easily reversed they shouldn't, especially if the OEM parts are sold with the car. They may make the market for a given vehicle even smaller though. I personally wouldn't want a car with only an RPI exhaust as it would be too noisy for me. However, I would buy a car with Remus back boxes over an otherwise identical vehicle with OEM boxes.
Of course, mods that suggest a car has been abused, mods that are homemade or mods that compromise function or reliability should br avoided.
If you liked the car but not the noise, it should be easy to sell the RPI exhaust here even if you stipulated that you wanted the buyer's OEM bits as well as cash.