There are four components to passer rating: completion percentage, yards per attempt, TDs per attempt, and INTs per attempt.
The “dink and dunk” passer that you describe benefits from throwing more high probability passes, thereby inflating his completion percentage, and minimizing his probability of INTs on such throws.
Also, yards per attempt is not the same as yards per completion or air yards attempted per pass. Yards per attempt does not necessarily prejudice the short passing game, as efficiency tends to balance itself; shorter throws lead to fewer incompletions and easier gains.
Wilson is ranked 6th in yards per attempt, while Rivers/Goff/Brees are ranked ahead of him at 3/4/5. The only qualifying QB with a wacko yards per attempt (9.6) is Ryan Fitzpatrick, and his QB rating is comparatively lower than the other QBs with high yards per attempt. This is because Fitzpatrick has a high rate of INTs per attempt, which is usually the dark side to the gunslinger approach.
That highlights the magic that Wilson has accomplished over seven season. He attempts a higher proportion of low-probability downfield throws, yet he maintains a plus completion percentage, an amazing TD rate, and (most remarkably) a low INT rate. This is what has set him apart in passer rating from any other QB in NFL history, except Aaron Rodgers. It should also be noted that Rodgers attempts a much higher proportion of safe “dink and drunk” throws, which also serves to undermine the premise of your argument.
http://www.espn.com/nfl/statistics/play ... ected=true