The problem with Sonic '06 is that it was developed in Japan. Sega is still afloat (somewhat...somehow) and prototypes can be thrown out all the time. Not only are there not many Japanese developers who speak English (frequently), but there are also strictly enforced policies when it comes to prototypes. There's also a decently size prototype gathering community in Japan from what I can tell, but again, there's not much motivation to dump these publicly (partially due to copyright law there).
In this case, we have so many Spongebob prototypes because those were part of a company auction. That company was Climax Group, headquartered in the UK. Since many of the people actively searching/dumping prototypes are from the US or Europe, it helped that we were able to find the relevant auctions for the game. Copyright is also strictly enforced, although in many cases, people set up servers in places where ROM distribution isn't nearly as strict.
That isn't to say Japanese companies don't do auctions, but most of us aren't aware of these things until it's too late.
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