The problem is, as stated already, the tubes/processing and not the milk issue itself is pure speculation at this point, unless such evidence is found. Even if the tubes/filtration they use is considered, we need to ask: is it enough to be the cause, since the milk isn't sitting long term in the tubes. From what I have read, it seems that the milk is processed relatively quickly though the tubes/filtration process, so we would need to ask if milk is moving that quickly, would it be enough to cause this, as well. Regardless, whether it is the milk itself or the filtration/plastic, the vast majority of milk is processed in similar ways, and there is enough evidence which raises concern, and so the effect for me is serious enough to seriously consider drinking less commercial milk and trying to fill my other half of calcium in with green broth, etc. I may even experiment going milk free for the time being. As long as I get enough calcium/magnesium elsewhere, I don't see it as a huge loss if I do ditch it for the time being. Milk makes Peating much easier, but I don't see it as being essential to Peating either as long as the minerals are covered elsewhere.
Note that it's not just milk that is affected: butter, yogurt, cream, etc. I personally don't consume milk but I keep consuming dairy despite this risk because I can't find an adequate substitute in terms of fat and protein.