Look who's writing about Mastercoin. http://gendal.wordpress.com/2013/11/10/decentralised-digital-asset-registers-mastercoin/
That's Richard Brown, Executive Architect IBM Banking and Financial markets.

Hi Richard, and thanks for this interesting article!

I just want to share a secret with you and your readers.
Mastercoin is not about the technology. It’s a project with a goal and a technology stack, which currently relies on Bitcoin.

However, that can be switched out or modified later if needed.

See http://wiki.mastercoin.org/index.php/FAQ#Does_Mastercoin_have_to_run_on_top_of_Bitcoin.3F

What about the bitcoins that go to the Exodus Address as part of every Mastercoin transaction? I'd rather not have that money go to an address controlled by any person or group of people (whose identities and motivations one can never be certain of). I mentioned this issue to dacoinminster a while back, and he said that he didn't think that very much money would come in that way; but even if it's only a small amount, it's a loose end, and in particular one that smacks of centralisation.

Note that Vitalik Buterin brought this matter up in his recent article on Mastercoin for Bitcoin magazine.

If one of the multi-sig outputs in a Class B (or C) transaction can be used to identify the transaction as a Mastercoin transaction, then there is no reason to have that output be spendable, right?