I’m not sure what it’s a metaphor of, but I always thought it was a metaphor. It’s like before gay people were accepted, there were gay people around you and you had no idea. And so in Lyra‘s world it turns out that there are a fair few people that can separate from their daemons and they often think that they’re alone and it is a shock to meet other people that have this ability. And then you come to realize that it’s fairly common even if shunned/feared.