Is there any reason an instance couldn't just copy Reddit's model? (Advertising that's hidden if you subscribe, paid awards, etc.)
The beauty of federation isn't that we have a million instances. It's that if there's a problem with one instance (such as greed), we can just go to another. In effect it adds competition instead of walled gardens.
Even if there's only a couple big instances that make up the majority of users it's not really a problem as long as the federation option holds. It's not the leaving that makes federation great, it's the ability to leave.
The app owners will work with him to prevent AI training from taking data from the site for free. And any issues the third party apps have doing that will be shared by the official app. They're not special in that regard. You can't really have public secrets behind a paywall. It doesn't really work.
There are many, many options here that are only being held back by Huffman's ego. Imagine losing billions in valuation because of personal ego. I bet investors are thrilled.