They walk a fine line. The Nest Atlas is questionable in itself. I think the reason there is not outrage is TSR is a great community for PoGo and they promote legit gameplay, while condone cheating. While their actions of sifting through the APK may be questionable, the reality is that it doesn't hurt anyone. In fact, it is our only real source of news/info on Pokemon Go, because Niantic does such a poor job communicating. That info isn't giving anyone a competitive advantage, plus things that are found in the datamines area already in the game, or soon to be implemented. It causes speculation more than anything or clarifies things about the game.
I think of it how the NFL condones gambling, yet works with fantasy sports and even has shows on fantasy football on their network. Those shows promote gambling and give people an inside advantage of how to do it. But the bottom line is, it's good for business.