You're right, I don't disagree with the assertion that long shots lead to long rebounds, and I disagree with the assertion that that somehow leads to fast breaks because EVERYONE starts moving in the other direction, and if you have more people on the perimeter when the shot comes off the rim you have more people able to stop the break.
The Knicks, Warriors, and Suns allow a ton of points on terrible percentages because of some combination of playing up-tempo (inevitably brings scoring totals up), they almost always play undersized (Stoudamire as a C on two of these teams, he is not one, David Lee is not a C and a terrible defender), they just don't have the players, and/or don't emphasize defense at all. The three really isn't a part of the equation.
To prove my point, the Magic shoot the most 3s per game in the NBA, and that's not pace-adjusted. The percentage of field goals they attempt that are 3-pointers leads the league by a significant amount, shooting 1/3 of their shots from behind the arc. They've been near the top of this statistic for years now. And they're usually also one of the top defensive teams as well. This year, they're leading the league in (least) points allowed, 6th in opponent FG%, and 3rd in opponent PPS. Dwight Howard is not the strict difference between those terrible defensive teams and arguably the best defensive team in the NBA.