By using phone numbers as IDs signal can rely on your phone's local contacts (meaning they don't have to send your social graph to their servers). This way they can keep very little metadata on you.
There's pretty much nothing for them to turn over except the fact that your phone number has the signal app.
Most of the other secure apps could turn over your entire contact list (which could be damaging for people in a protest that are being targeted).
Confirming a single phone number has the app is not nearly as big of a deal (I'd argue it doesn't matter at all).
But that doesn't help much if the entire contact list is a list of trash mail adresses (in the case of Wire) or a list of random IDs (in the case of Threema). And at least Threema does not store any information about your contacts on their servers.
Can you obtain a phone number without any ID in the US? Because you can't in large parts of Europe.