No, on reading it, they also mention "the leaching out of oligosaccharides into a warm, slightly basic soak water", followed in the next paragraph of the specification of a pH between 6.5 and 9.0 ("slightly acidic to alkaline" - meaning preferably alkaline but slight acidity is OK if you don't go too far).
Oh, there are actually 2 recommendations, one for oligosaccharides (as you correctly stated), but also, if you look at the sidebar: "Neutralizing Phytic Acid" It recommends soaking in an acidic solution (for that purpose). So it seems like the ideal according to this article would be to start soaking basic, then acidic, then slow cook.
Actually, it seems to me that if you were really serious, you'd soak for 6 to 12 hours in a basic solution to leach out oligosaccharides, then ferment with a prepared solution for another 12 to break down phytic acid, and then cook.
But wow - this is a great article!