As long as they can get it to produce a signed iPhone executable, there's no reason it wouldn't be allowed. Game engines like Unity and Torque already do essentially the same thing that Real Basic would have to do.
The SDK and app development agreements do not allow everything, even if it's a signed executable. Read sections 3.x.x of the SDK agreement.
And just because other similar apps have been accepted in the past does not mean that a similar app won't be rejected in the future for violating one of their (newer) interpretations of the agreement.
Eventually it probably will. But for right now their version that builds Cocoa apps hasn't even been released yet, so it's going to be awhile before they get around to building Cocoa Touch apps.