Great question, eddie. The short answer (according to my understanding) is that it doesn't matter right now, for two main reasons.
First, because an asset like LTBcoin can be migrated at a later stage to a different system when the technology becomes available. I'm grossly simplifying here, but it's a bit like moving your digital photo from CDs, to DVDs, to SSD media.You change the underlying storage and the protocol you use to access and handle your data, but your photos are independent of that. In the same way, a public ledger that keeps track of which addresses holds what assets is ultimately data and independent of how it is stored.
The second reason is that services like Counterparty and Mastercoin could also choose to migrate to a sidechain as described in the episode if it becomes feasible to do so. Again, this is possible because these systems are really just data and protocols to handle that data. In such a case, they would probably be able to retain their native currency if necessary and, while that would be less efficient than using Bitcoin, there could be a good reason to do this that I'll cover in a minute.
Should Counterparty, Mastercoin, etc. adopt Bitcoin on their own sidechains as their currency, XCP, MSC and so on would probably become shares in their respective systems. Owners of XCP, MSC and so on would receive dividends in Bitcoin from transaction fees on these sidechains, as well as from any fees levied on bitcoins moving in and of out of the sidechains from the main Bitcoin blockchain. This means that you could even have a scenario with an exchange rate between, say, Counterparty bitcoins and Bitcoin bitcoins, which will depend on the relative demand of each and the cost of converting one to the other.
The most obvious downside to this second scenario is the added cost from the sidechain transaction fees, which is why I said before it could make good sense for sidechain protocols to keep their own internal currencies that get their value from pure supply and demand. I think we will see both kinds of solutions and market forces will play a part in deciding which prevail.
Of course, there is also the possibility of sidechain protocols that decide not to impose any fees of their own on top of the standard Bticoin transaction fees. However that would be the same as (and just as far fetched as) someone forking Counterparty or Mastercoin and making XCP or MSC unlimited in supply and freely available from a faucet.
With all that said, there's one other big issue that I wish had been discussed in more detail in Episode 99, which is the problem of the security of sidechains. Even with the proposed merged mining solution, you have all sidechains at the mercy of the large pool operators, who will probably have their own vested interests in specific sidechains. That's definitely far from ideal.
That's probably more of an answer than you were looking for, but it's a fascinating topic and I'd love to see what other people think.
