I can explain how it can be done. Let's say you need a new dependency. You can't just add it to the project. Management would kill you. There's a lot of checks you have to make. Like licenses and signatures.
In this case, you're concerned about signatures. I'll stick to that. If I believe I need crossenv, I see it advertises kent@doddsfamily.com as the author. I look up Kent Dodds. I find various bits of information about him. I find his twitter @kentcdodds for instance. He may even have a page published @doddsfamily.com to verify his key.
If the key has been around for a while, that's probably sufficient for me. If he doesn't have such a page, I send him a polite message, "Hi Kent. I'm evaluating your software for use in my project. Can I get you to verify your key please?" and Kent is a professional, so he agrees. I send kent@doddsfamily.com an encrypted message and he sends me an encrypted reply. Done. I'm satisfied that he controls the key.
At this point... oh, wow. That's not my key! Did you say crossenv? My package is cross-env! Alert the Node authorities! There's a malicious package pretending to be mine!
Is that 100% infallible? No, but here's the great thing. Even though my verification system may not be bulletproof, others with resources like DoD or FBI are out there verifying keys. They'll go see Mr Dodds, in person, if they have to. In this way, key verification is a bit like herd immunity. And the older the key is, the more trustworthy it probably is.
People who are here arguing against this system have a few things in common. They don't propose a better system, because they don't have one. They're also a bit like anti-vaxers. They irrationally refuse to participate in such a system to everyone elses' detriment. They're a bit like congress as well. They can't just look at a working system like single payer, and copy it. They refuse to accept that this is the best available option, so they fold their arms and actively fight any attempt to implement it, as is the case on that github 4016 issue.
So now that I've maybe offended everyone, strike me down with down votes. That's the basics of how I would go about it though.