You've misunderstood a lot of Latacora's critique, but I think the most important point you've misunderstood is "negotiation."
> PGP does not do negotiation. It can't. PGP supports asynchronous store and forward applications. It works over a one way channel. Your cipher, digest, and compression preferences come along with your public key They are signed and so are protected by the base cryptographic system. An adversary would have to break the cryptography to modify your preferences.
> I do not agree that compatibility is a bad thing. PGP is actually a good example of how to deal with backwards compatibility in a good way.
"Negotiation" here doesn't mean a synchronous back-and-forth conversation. "Negotiation" in this case means, "if you're not sending me the most secure version, I'll just accept a somewhat less secure version."
PGP encrypted messages are "take it or leave it," but that doesn't mean that PGP doesn't do negotiation. Instead, it means that the PGP implementations decide how much insecurity to accept in favor of backwards compatibility.
Here, in the blog post linked at the top of this page, Sequoia moans that they can't bring themselves to turn off SHA-1 because Debian developers use it. They're accepting a less-secure implementation for backwards compatibility. It's right there in TFA.
I'll tell you what: instead of "don't use PGP," how about "Don't use SHA-1 and don't use any tool that accepts SHA-1 by default." Today, in 2020, that means "don't use GPG, and don't use Sequoia PGP" and I'm confident that it means "don't use PGP ever again," but you and I don't have to agree on that.
The fact that you can change the defaults to be more secure and less backwards compatible doesn't make PGP safe to use. It's dangerous by default. Don't use it, and don't advocate that others use it, until PGP is secure by default (in other words, never).
The other thing you've misunderstood is the problem with long-term keys.
> Most people prefer to keep their identity indefinitely. That is why, say, the Signal protocol also has a “practically-forever root key tied to their identity”. It is inherent to the problem.
No. Long-term public identifiers are indeed, desirable, but PGP's public identifiers are paired with secret keys. Tying your identity to your public key means that you can't change your secret key unless you change your public identifier as well. (In Signal terms, that would be like saying that you can't rotate your secret key without changing your public phone number, which would be absurd.)