I don't think anyone's discounting those facts. Yet Tony could have chose to be a power hitter, just like he chose against signing with another club for more money.
In fact, Ted Williams chided Gwynn as a "big man" for his underutilized ability to hit for way more power. In fact, when Ted named his top twenty hitters list, Tony was the only currently active player invited.
Yet Tony was more satisfied being the ultimate role/team player and the average HOF WAR accompanying it.
What some are trying to explain is how Gwynn was one of the purest hitters in the game. I personally think he's is one of the few players who transcend WAR as a measurement, by choice.
Just listen to what Ted Williams had to say about/to Tony reaching .400.
https://www.youtube.com/watch?v=K3hLiyNSISQ