If I wanted to buy a car I know would last, I would NOT buy a modded car.
Mods are almost always a sign of heavy/aggressive driving. People who granny their car and treat it the best they can aren't adding all those extra performance parts.
Of course there are exceptions to the rule, but I think it generally is true. All my friends who have modified their car in some way are not feather footed.
So seeing a modified car that is suppost to be a limited production vehicle, you know it is going to be one of the first ones to die as its being pushed harder then its unmodded brothers/sisters. As such it would likely lower the perceived value even though it has had more money put into it.
However, that isn't always true and now and again you will find someone who wanted to do all that work and as such it can save them time and money..