The linked document merely explains the complexity we observe in the genetic interplay of individuals with 'other than brown or blue' alleles.
The doctor concludes the article with the concession that the model he outlines in place of the layman's Mendelian model (which remains very useful, in my opinion) still does not explain two blue eyed people producing a brown-eyed offspring.
The question I'd like to see answered is 'where is this mythical brown-eyed offspring of two blue-eyed parents, and how well does the father trust the mother?' lol
Nature is full of surprises, so I'm not going to say it isn't possible, but I'll believe it when I see it.
PS Evidence suggests the Japanese, like the Mongols, to have some European genes. Politically suppressed evidence indicates that prehistoric Europeans wandered the globe and left their culture/technology behind.