I am willing to stipulate "short of running everything over Tor" for the sake of argument.
The reasons for avoiding Signal (metadata leakage, mandatory phone number usage, questionable 3rd party dependencies, etc) are valid, despite how I often argue to the contrary in favor of getting as many people on Signal as possible and using it for daily communication. Talking common sense to this demographic is hard though, in the context of basic security concerns persisting year after year.
On the flipside, the phone number as identifier issue has caused apps like Kik (super popular among the gay community, despite shit security), Wickr and Wire to become popular among the non-tech demographics, which is extremely disheartening.
It is totally OK if you are extremely worried about hypothetical scenarios where the phone number you used to register to the Signal network can be correlated to your physical location and then a gas station camera filmed you and then all is lost; but I want to believe that really at risk people are smarter than that, and just get a burner phone and even pay a homeless person a few bucks to buy it for them.
There are also ways to get a phone number through the Internet, so you don't even have to go to a physical location to buy it.
I think that's why Signal isn't prioritizing this right now, phone numbers can be a problem? yes. Is it hard to get a fake phone number that is not traceable to you? not really. Next problem please.
I think Signal is achieving the goal of being the default go-to secure messenger. I'm sure, even technical people who like to nerd out on alternatives, faced with a real world risky situation when they have to communicate with a non-technical person, would recommend Signal without a second thought.