Now that Ive gotten my obligatory yellow correction post out of the way, heres my view on the subject; Mods should be done out of passion, with no hope of recouping the initial cost. The more that's done to a car, the narrower the prospective buyer list becomes. That being said, given the choice of a stock car vs a fully modded car, built exactly the way a potential buyer would do it, I could see someone paying slightly more for the built car. It would save them a ton of money that could then be used for even more mods!
Or they may not be the DIY type and would prefer something already built. In the end it just turns into a waiting game. I on the other hand picked my car because of the low number of mods, among other things, since I am the DIY type and enjoy project cars. If your hoping to cash in on built cars as an investment, I have a great revenue sharing/auto-surfing opportunity for you.