That's exactly what prosody is doing, but it's a weird solution. Essentially, they're just ignoring the missing EKU flag and pretend it would be there, violating the spec.

It seems weird to first remove the flag and then tell everyone to update their servers to ignore the removal. Then why remove it in the first place?

Yes, this is what is happening. It isn't happening fast enough, so some implementations (especially servers that don't upgrade often enough, or running long-term-support OS flavors) will still be affected. This is the impact that the original article is warning about.

My point was that this is yet another change that makes TLS operations harder for non-Web use cases, with the "benefit" to the WebPKI being the removal of a hypothetical complexity, motivated by examples that indeed should have used a private PKI in the first place.