Yes. Twitter silencing a user on their own isn't the same as Twitter silencing a user due to a government order.
When Twitter's defense against the government's request is because of the ideal of free speech, not the First Amendment but the ideal that it is based on that predates the First Amendment, then it is worth pointing out the double standard in Twitter's own behavior not upholding that ideal.
That said, Twitter having a double standard does not invalidate their argument. From a purely logical perspective, an argument does not depend upon who says it or why they say it. But rarely are people interacting on that purely logical level, and so Twitter's double standard does allow us to both poke fun at Twitter and to call into question their actual reasoning as potentially being different than their stated reasoning.
There's no double standard though. This is like saying: "how can a newspaper say they're in favor of free speech if they're not willing to publish any story that's submitted to them?"
Twitter can support free speech by advocating for their right to control their platform, and for other people to have the right to create their own platforms and put content on it. The government using strong-arm tactics to unmask critics is a threat to free speech through any medium.
The US is asking for the identities, because they suspect someone is impersonating a federal agent. The government has made NO REQUEST to shut down the account.