I don't think that explains everything. I think that if Honda pushed this technology through they could have bikes in every category of motorcycling, from sport bikes through enduros, that would have big advantages over everything else a man could buy, and that would land them massive market share. Although they wouldn't make as much per bike, they'd sell a lot of them, undercut the competition, and make money that way. And they could probably even put a fairly hefty price on them and still sell tons, because the public would be willing to pay a bit of a premium for The Best. I speculate that the other members of the Big Five would've been much more likely to run with the line if they had invented this, and not Honda. Honda is, as far as I know, the only company that has flatly and openly admitted to being pro-four-stroke on a fundamental level, even quite early on.
The warehouses of empty bikes are proving that four-strokes are not a money-making business strategy in motocross at this time, and without the change to the rules they never would have been at all. I don't know the story on why street-bikes went 4T but I'm guessing it's emissions. This Honda engine would solve the problem on the street, and I would guess that it'd have the big, smooth power to seriously lay down the gauntlet in motocross, handicap be damned.
No, I think dollar-signs-in-the-eyes would've caused a company to roll ahead, patent the thing, and start stamping them out to the tune of their competitors' death moans. But there is an internal set of priorities at work here in this particular situation.