If I'd be a spying agency I'd do just that - develop "secure" app that would collect unique identity of every user. Verified phone number is a perfect unique ID.
"Just give your phone number to us, and don't worry, we won't share it with anyone!".
That exactly what Signal does.
Until they allow user-created ID's with no link to any identity - the above concern stays.
But a phone number isn't supposed to be secret, it's supposed to be given to people to contact them. I don't see the nefarious use here. Can they determine I'm a Signal user? Sure, but they can get that from IP address, App/Play Store installs, etc.
In many countries the government and the company that you register the number with need to know who you are (or can deduce it from the place where you are connecting).
Yes, but people in those countries can buy a US VoIP number from a US vendor for $2 and use that as their Signal number.
You don't need to use a GSM number, and you don't need to use the country code in which you live. The fact is, mostly anonymous phone numbers are available on the internet for use with Signal, and Signal (correctly) does not discriminate on country code or "type" of number. Any number that can receive phone calls or texts will do.
There are indeed countries that want to tie phone numbers to strong identity, but you can simply get a second number from a country that's not so hellbent on restricting access.
The number you're logged in to in Signal on a phone does not need to be the same number of the SIM card inside that phone. You can use any number you wish.
"Just give your phone number to us, and don't worry, we won't share it with anyone!".
That exactly what Signal does.
Until they allow user-created ID's with no link to any identity - the above concern stays.