They have good cause to believe you’re a Signal user, so they get a judge to authorize a subpoena based on your phone number, and Signal complies - and, yes, all they’re doing is confirming to the FBI that you have an account with them.

Literally all they need to do is have their own phone with Signal installed, and then create an address book listing with the Suspects phone number on it.
Next time Signal syncs, it will pop up “Suspect is on Signal!”.
Subpoena-ing the Signal Foundation is not required.

But it proves nothing, and if you are in a jurisdiction where the police can demand your phone or you are stupid enough to hand it over when they can’t, that’s not on Signal.