Correlation does not imply causation. Intelligence comes in all kinds of forms, which is why you have people with PhDs struggle with their tax returns or musical geniuses who struggle with maths. The Wonderlic, according to your own article, is just a measure of how good someone is academically. The article itself says the only value of the Wonderlic is that it's a standard test so everyone can have a common baseline (and yes, I think the significance of the combine is highly overrated too), which doesn't mean anything if that common baseline doesn't have anything to do with making pre-snap adjustments and having the spatial awareness to see what a defender's going to do.
No control has been made for the general upbringing of most QBs including which high schools they went to and other factors that affect their academic performance but not necessarily how good they are as a QB (and there are an awful lot of Stanfords, USCs and Cals on that list) so if most QBs score high but also tend to be in better-off families and go to better schools than those in other positions, that'll skew the Wonderlic scores of the position. Just because there isn't a big body of evidence of QBs with low scores (which seems to be the main thrust of your argument and the literature you cite) doesn't mean a low score translates to poor NFL play.
I said on the first page that there's a huge bust potential, but if he does bust it won't be anything to do with the Wonderlic. But I'll bear in mind his Wonderlic score next time he has a few seconds to calculate how far a train can travel in 4 seconds.