I read it as that’s also the point. Adding formal verification is not a strict defense against bugs. It is in a way similar to having 100% test coverage and finding bugs in your untested edge cases.
I don’t think the author is attempting to decry formal verification, but I think it a good message in the article everyone should keep in mind that safety is a larger, whole system process and bugs live in the cracks and interfaces.
You're right. It just seems as though it should be self-evident. Especially to those sophisticated enough to understand and employ formal verification.