Why would anyone bother customizing a car in GTA? It's just going to get exploded within 30 minutes of whatever mission/random chaos you embark on next. Unless it's persistent and will always respawn in, say, a particular house's garage, like you've got a taste for a certain souped-up mustang and it's like you're constantly rebuying them after the last one got blown up in a shootout.
I think this is pretty key here. With the reintroduction of garages, I'm hoping for some persistence in cars, at least for one character (say, Franklin). Saints Row 1 improved car persistence from the GTA games and I thought that GTA IV would end up borrowing the concept from them, where your cars are accessible in any of your garages, except they aren't automagically fixed up when you enter and exit the garage... you have to pay a small fee for those repairs. It really gave you a sense of vehicle ownership.
GTA IV took a big step back with this. Not only weren't their actual garages, but car ownership was practically nonexistence. I think you that you could park your car in front of your apartment in a designated spot, but it wasn't the same as in San Andreas where garages were obvious and worked consistently. I still think I'd park a rare car outside my apartment, and when I'd come out, it would change into an SUV.
So, with vehicle mods, I'm suspecting that Rockstar will be implementing some sort of vehicle ownership system... Even if maybe it's just for when you're racing or for designated times in the game. I just can't imagine implementing a robust modification system ALA Midnight Club, and then have the player junk every car like usual.