I created a new BIP draft relating to this.

https://github.com/TierNolan/bips/blob/bip4x/bip-atom.mediawiki

The latest version allows transfers between chains as long as 1 of them supports non-standard transactions.

This means that fast testnet <-> mainnet transfers would be possible. 

Testnet would have to have the longer timeout, since it is the network that supports non-standard transactions.  Everything on Bitcoin would standard.

I am going to look into creating a simple client/server this week-end to verify that the scheme actually works.

What is cool about this is that it means that a BTC <-> altcoin trading system would only require that the altcoin accepts the non-standard transactions template. 

It should be much easier to convince an altcoin dev to make the change than updating the Bitcoin reference client's rules (though hopefully, they will too).