You can have many different programs in nats, meaning for example "50% revshare" and "60% revshare" and "no consoles" and whatnot, and you can assign different sites to the different programs, and have different join pages / payment terms / etc on each.

I do know that if a program is set up as "non public" then a given affiliate will only see the program if the program owner sets him up to use it, but I don't know if you could, by default, set up so that people going to affiliateprogram1.com would be unaware that there is an affiliateprogram2.com also running under the same NATS installation, and with a different appearance.

As Darling said, it would probably not be difficult to do, but since NATS is all Zend encoded, they would have to provide you with the necessary "hooks" to be able to modify it to do what you're asking, and my guess is they would not be willing to do that.