Good point. Most of the low carb diets I have seen (with exception of some Paleo & SCD), are fully focused on the carb amount. Whereas the previous 2 focus on the carb TYPE. Even in Lutz's experiments with low carb on diabetes and IBD, his approach (carb restriction but allow any type) took people years longer to heal (8 years compared with 1-2 on a Paleo diet).. with these approaches (carb level such as Atkins, Lutz) someone can eat any carb/fat no matter how frankensteined (such as aspartame,hydrogenated fat, corn/wheat/soy extracts etc.) but just in low amounts. What's worse is that some of these "diets" sell "health bars" with such horrid ingredients, on the basis that they're OK since they have a great Carb-to-Protein-Fat ration!
The other paleo/SCD approach totally eliminates possibly dangerous foreign proteins entering the body.
Your other point about a lot of troublesome proteins coming from "new world foods" was also valid, and there's info around to back it up.. it was reported that the Inca's actually fed potatoes, tomatoes and eggplant to the Spanish invaders to WEAKEN them! (Interesting) Further, some people on the list advocate eating potatoes, yams, sweetpotatoes etc.. however, these have only been known in the West for 1000 years or less.. making them a very new food for about 90% of people's digestive system.

reg.,
Dean, Oz.
>>
The original edition of Neanderthin hardly mentioned carbs in fact. The
emphasis was in avoiding foreign proteins.
This is the big element missing in Atkins. 
>>