I'm curious how much agitation he did to the two batches. When I started doing Low O2 batches I didn't touch the mash at all, I just ran the water in and let it sit there for fear of stirring in too much O2. I have since started to stir it some but not too much and noticed a modest efficiency increase.
I didn't see any indication in the article of how much mixing he did, so I'm curious if the low o2 version of it just wasn't mixed in as well and he got poor efficiency from that. I did see that the normal one followed the water in first, then add grain method which would probably ensure that he had good mixing.