Jon Dorn, the editor of Backpacker, is a member of VFTT and has responded to posts here before.
From my dealings with the magazine as a photographer, my impression is that they do a very good job of trying to be environmentally responsible in their coverage, but mistakes do happen. Photographers who submit materials also have to make sure they act in an environmentally responsible manner when they are out shooting for the magazine, and resist the temptation to break the rules in order to get "the killer shot".
Also, I imagine it's a tough balancing act trying to feature "new" places without spoiling the "secret" ones, while attempting to satisfy the broad range of backcountry users that read their magazine.