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).
There's nothing inherent in phone numbers here. Both iOS and Android also allows you to add e-mail addresses (and other identifiers) to your local contacts. I'm yet to hear an argument as to why e-mail addresses or other identifiers can't be used in addition to phone numbers, or why it would be a complicating factor.