In our PADI shop, we use the same gear as the students when we teach, which is standard rec gear. Since in our area probably 95% are preparing for tropical locations in mostly rented gear, it makes a lot of sense for them to train in that. It is not a sales thing--our shop sells BP/W's as well.
In the academic portion of the class, I show and explain all sorts of equipment they may encounter or consider purchasing. I explain the the thinking behind long hoses and bungeed necklaces.
In the pool, I now do very little on the knees, starting right from the start in the shallow end. I think people started doing things on the knees decades ago because someone thought it was a good way to start, and it became a habit. People now are have trouble visualizing a class done differently. In truth, it is much easier to do many skills, like regulator recovery, when students are in something close to a fin pivot position. It makes the regulator drop to a more natural position when released. Students on their knees frequently lean backwards, so their tanks pull away from their bodies in a way that is not at all like real diving.
In summary, I don't see PADI and DIR as fundamentally opposed at all. I do, however, think that PADI instruction has to think that it is preparing students for what they are likely to encounter when they go out diving. Many of you live in locations, like the Pacific Northwest, where many people dive the DIR way or similar. That is not what my students will generally see. I myself have hundreds of dives in dive locations (see my profile) frequented by dive vacationers. I am pretty sure I have never seen any more than 7-8 bp/W's total on those trips, and almost every one of them was someone with whom I prearranged a meeting through Scuba Board.