If Signal receives a government request for information about an account based on an active username, Signal will be able to hand over that account’s phone number along with its creation date and last connection date. So being able to use Signal through usernames doesn’t mean your phone number becomes subpoena-proof — at least not without using the new ability to change your username at will.
That's the most important part right there. Signal can convert a (current) username into a phone number, but not the other way around. (Would it be theoretically possible for them to hold a username history?)
It's a real shame the usernames and phone numbers weren't connected to a completely different ID in their system, but I'm sure there would be issues with that too. The username thing is already quite the advancement.
Granted, this is already leaps and bounds beyond what Telegram does for usernames.