Of course there's no protection on CS2, there's no HW on the carts to prevent the roms from being dumped. now I don't have CS2 (preordered or otherwise) so I don't know this but I can imagine the roms being serialized (Paid Unibios leverages this to avoid dumps/piracy, Right?). There has been no solid confirmation that the roms will be officially provided (I've, in addition to Others, have asked this with no solid confirmation other than 'Don't worry about it') so Until this has been confirmed by you that yes, they will, I can only assume that CS2 usage either in a conversion not purchased from you/neobitz or in a multicart like you would not only be unauthorized, but publicly discouraged by you (justifiedly so).
This would also be the same with NG
evTeam's games.. Really expensive, limited runs of ORIGINAL games and no rom release. This is where no one should argue that unauthorized use of their games, or dumping them for repros/conversion is ok. It's NOT ok. The second hand market is nearly as bad. When the games go out of print, they're sold for ridiculous amounts of money, none of which ever gets back to the people that worked on it.
People work hard on original IPs and should be paid for their work. Directly
Things like these is what leads me to believe that due to the 'piracy' concerns you would prevent this cart from being used with your Unibios. The way around this, creating a sort of Neo-Geo homebrew marketplace with individualized serials only installable on a specific cart (with a sort of public/private key encryption/decryption on the cart) would be great, but it would be expensive, convoluted and impractical (for both HW and SW) for such a niche product.
It
is standard stuff, and it needs to be openly discussed. I'm glad we're talking about it, especially since the HW hasn't even been produced yet.