Now this is going to be the restriction.... what is the point in having the code as open source if you cant implement it?
Well... (since I had similar concerns) as Paul said, if you "clone" the board using the 8u2 chip then we think you're allowed to use the vID/pID combination given to you by the 8u2 chip manufacturer. NOT Arduino's own. That's fair enough if true.
Or if you choose to put in the old FTDI chips instead, there's nothing in the new bootloader that's going to mean you have to write your own one of them. And we know the IDE will still be happy.
So actually... things aren't as half a grim as they looked. People may say a few of us were whinging, but from that we got lots of good info. Information that would have come out anyway... but I like to think we expediated the process. 