A lot of interesting speculation in this thread. It's probably a combo of "all of the above".
It is pretty common for the mfgs to do some last-minute shenanigans to the tuning of a bike to get the bike comfortably under emissions and noise restrictions. And Yamaha may be anticipating future ratcheting down of regs. If they can produce a bike now that meets the future regs without modification later, then potentially they can save a lot of money. Same with building a single basic tune that can meet the differing regs of various markets - different regs that may vary in stringency in different areas. I see a lot of things in the S10 which strike me as watching the proverbial bottom-line for costs very closely so the bike can maintain a cost advantage over the competition in a time where the exchange rates are not favorable to Japanese products. This may be one of them.
Could Yamaha have gotten this bike past noise and emissions regs w/o the restriction? Probably yes, but it might cost more money long-term.
With today's fly-by-wire throttles, there is also a good rationale for doing this sort of restriction simply to make the bike more controllable for the intended market. With many of today's super-powerful bikes, there is almost no point in providing full power in the lower gears as most riders simply can't put the power to the ground - they either get wheelspin or a wheelie. Now the S10 makes pretty modest power and putting a full 90 RWHP to the ground in the first three gears seems pretty reasonable to me, but Yamaha may feel differently.
If you're ruthlessly practical about it, about the only thing having prodigious power in the lower gears does for you is jerk your arms harder - there really aren't very many places where you can use 90-hp in 1st gear in a practical way. Where big power pays off is in high-speed work where you want to get good acceleration doing 80+ mph and/or using the power to tackle loads/grades - in these situations, presumably you're in a higher gear and the restriction doesn't apply. I'm not terribly bothered by the restriction, although I wish it wasn't there.
In a lesser way, this strikes me about like the 186 mph top speed limiter on superbikes like the Busa and ZX14. Do I like the electronic nanny that the mfg has put there to protect me from myself? No. Practically speaking, is it enough of a real problem in everyday use of the bike that I'm going to go to any trouble to remove it. No.
But.... if we get a good US-based distributor of the mod, independent testing shows the mod works well and has no bad side effects, and the costs come down, I'll probably be a player.
- Mark