The problem with modded cars isn't so much that it's modded. People often look for a car with more power for that reason. The problem in selling a modded car is you have to have good documentation and references to make the car marketable. Simply dropping a modded car with a long list of mods for sale is doing nobody any good, this is including the seller. The biggest problem with a modded car is when something goes wrong with it. For example, a CEL shows up and it's warning against some type of fuel delivery problem. If you don't have the exact breakdown of the build, you'll spend time trying to figure out of it's a fuel pump, injector, problem with the spark plug or the tune. If you don't have documentation or references to help you blueprint the build, trying to sort out a common problem can turn into a complex task that costs a lot of money.
Of course, similarly with large builds, not all builds are quality builds. On the S550 Mustang, for example, I've seen numerous issues where people with an aftermarket blower would bring their car in with multi cylinder misfires. More often than not, I'd pull the plugs and only 6 would be one step colder plugs. The back 2, which can be a PITA to get to, are often left stock by some two-cent mod shops. I've also seen a lot of people claiming their car had an aftermarket cam, only to find that it was just a ghost cam tune. Thus, when a person buys a modded car, they're also buying the work the owner or a shop did on the car... potential cut corners and and all. I
This is what turns a lot of people off to modded cars. We don't mind modding cars usually, but people like me have problems with other peoples' work. I have never bought a modded car from an owner who didn't know the build inside and out. For example, the type of person who pays a shop 20 grand to build their car, then they drive it 5 times a year and don't really know anything about what was done and why. If the car ever has an issue, I'd basically be left at square one trying to decipher what the heck was done, really. That's because more often than not, what the owner says was done is usually not really what was done in its entirety. On modded cars, there's a lot of devils in a lot of details on some of them.