According to my parts list, there are two different airbox lower halves. 17231-300-040 is for America, England and Australia whilst 17231-300-620 is for France, Germany, Holland. I believe the difference is the intake as you have observed.
The problem I have experienced with three hole upper and original lowers not mating correctly has been with the LPM replica airbox as supplied by David Silver Spares. The Yamiya airboxes are undoubtedly more accurate.
Chris R.