These libraries aren't using protocols for type safety though, they're using them as a performance optimization. That's certainly a perfectly fine reason to use protocols, and I agree that it's a completely legitimate use case. It's the whole right tool for the job thing. If you're writing something where performance is the top concern, then that's what protocols are for.
I very much agree with you that that there are people who focus on low level code, and those who focus on application level code. The style of coding will be different depending on the type of problem you're solving. You're right that I failed to qualify my original statement regarding protocols being an anti-pattern.
You're absolutely correct that we should take a pragmatic approach towards using language features. Hence why the context of whether protocols are the right tool to each for lies in the type of code you're writing. And of course, some people find it easier to have more structure to help with their reasoning. Although, I'd argue tools like Malli work better there.
To sum up, I'm not arguing against protocols being useful or that there's no place for them. We started this discussion talking about whether protocols provide equivalent guarantees to Java's type system. I disagree regarding that. However, I also don't think that this is a real problem. Otherwise, use of something like core.typed would've become prevalent by now.