You're missing the point of the article. A particular smart contract, or zk-snarks, or a new Bitcoin protocol functionality... these are not application layers,

You're missing the point of the article. A particular smart contract, or zk-snarks, or a new Bitcoin protocol functionality... these are not application layers, they are a particular application. Lightning is an application layer that enables a whole new set of applications. And this is groundbreaking stuff, you can't expect it to have been released in Bitcoin's original 2009 client.