I suppose mods will have to be judged individually depending on how much they affect the game. If a mod arrives that makes the game a totally different proposition then maybe it could be listed as a new game for the purposes of the Pinside rating system, similar to the way Stern Pros and LEs are. I don't think there are currently any mods that would justify that yet.
Ultimately, all the reviews written are already based on playing a wide variety of machines in differing conditions. Some will be horribly worn with lights out and weak flippers and some will be dialled in perfectly with all mods and LEDs and whatever so I wouldn't worry because, once enough reviews and ratings are made it will all average out.