Really sorry to hear that your surgery hasn't been entirely effective. :( I wish you less suffering, soon.
I'm definitely a newbie in all of this, but the science does point to low levels of stomach acid being the culprit. It's suggested that low acid creates a poor digestive environment in the gut, which can actually cause pressure/bacteria that leads to reflux (even if you had too MUCH acid, it shouldn't come up the esophagus, although there is a disease (rare) in which it does). The PPIs, in shutting the acid off (and contributing to a host of other ills, as you've mentioned), are making the problem worse. It would seem that the real answer lies in not LETTING that acid get to the esophagus, NOT shutting it off. Easy, right? ;)
A comment that was made on that article also suggested (based on some research) that low acidity can cause less accessbility of food into the small intestines, thus causing gastric delay and, thus, reflux back up the throat. Yuck!
*However*...What to do when diet, natural treatments, etc., have failed? And when surgery hasn't even worked well? I don't know, and I don't pretend to have an answer. I'm a recent LPR sufferer, and I worry that I won't be able to control it, that it will control my life. It's awful.
I don't know--maybe having lower stomach acid (or none? Although that can't be possible, right?) is better than dealing with reflux, if nothing else works. I certainly can't imagine life with the constant reflux, weight loss, etc. So, these are just questions I'm looking at, and not claiming to have the answer.
I do hope you feel better, soon. Such a difficult disease.