That assumption isn't necessarily possible. The advances might not be able to be incorporated into the Bitcoin block chain for technical and/or vested interests reasons.
Even if the technology is completely different, a technical hack could be done with lots of if/else statements in the code:
if( the input transaction is of the old format )
use this code taken mostly from the old Bitcoin code
then convert it into an input of the new format..
else
just use the new, incompatible code
...it'd be very hard to come up with a technological change that made that sort of hack impossible.
Well this might be me personally, but I see the entire layer build on top of Bitcoin, separate from Bitcoin itself. Because all that those layers do, is build on the Bitcoin API. Where the Bitcoin client is forcibly delayed by hardforks, I don't see any reason for the infrastructure on top of it, to be so depended on specifically Bitcoin. (Hardfork means at least 6 months, before it can be enforced) While everything build on top of it, just needs to recheck all the API hooks, and can technically be ready to go again in a matter of hours/days.
I think you're vastly underestimating the complexity of switching to a new coin. Look at how long it has taken Mt. Gox to add Litecoin support. Litecoin is almost identical to Bitcoin. One might think that it should take them a day or two. But there's a lot of hidden complexity if things weren't engineered from the ground up to support multiple coins. I also think 6 months is a very long estimate for a Bitcoin hard fork time, given that the Bitcoin devs would have the source code of the new coin.
I think we can use another way to include Bitcoin block chain in Bitcoin3 with lower complexity.
The new Bitcoin3 can have a protocol compatible with Bitcoin network and accept to exchange your Bitcoin into Bitcoin3 with 1:1 exchange rate.
The protocol defined a plain text and valid Bitcoin address like 1YouCanGetBitcoin3BySendBitcoinHere to ensure that no one owns its private key.
And if bitcoin owner send bitcoin to this black hole address, Bitcoin3 protocol will create new Bitcoin3 coin and bind to the owner's Bitcoin3 address.
Then the new Bitcoin3 coin can run a completely new block chain or blockcahin-like structure and any other crypt algorithms.