Because they are not different platforms, they are just regional naming differences for the same platform. Our database is US based so platforms like that inherit the US name, all the games from other regions are still in there, just marked with Japan as the region. So scraping PC Engine as Turbografx-16 is no different than scraping it as PC Engine in the first place the as games are still there.
I have to do the same thing with Sega Genesis, i'm in England, and there was no such thing as the Sega Genesis here, it was the Sega Mega Drive, just like Japan. So i called the platform "Sega Mega Drive" and scraped as "Sega Genesis" in order to get all the games scraped correctly.
Launchbox imports exactly the files you tell it to, and who is to say that the Hyperspin list is actually a accurate list itself? No-Intro romsets get updated often with new games also often added, so i wouldnt take a old Hyperspin list as gospel. If you seem to have less games than you think then they were probably just conbined, which is a option in the importer that is checked by default. So for example Mega Man and Rock Man are the same game with a regional naming difference, and again as the database is US based you will have Mega Man in NES, and if you right click that game you will also see Rock Man.