It's worth noting:
This isn't simply some mistake or oversight to be fixed.
This is a result of an intention, and the affect that had on what's worth prioritizing.
You are not meant to have people joining in progress saves for single sessions, and those saves to continue without them.
This is NOT a drop in, drop out, doesn't matter no impact, session based kind of game. It's too story driven for that.
This is a consistent party, for the whole save, always together or not playing that run kind of game.
You aren't supposed to be joining friends, or having friends join solo saves just for a bit then leave while the save continues solo.
You are supposed to have a multiplayer save, a separate one for that particular set of friends, only played when the whole group is playing, doing a co op run of the story where the story is that the characters you chose at the start are a consistent group.
Your friend's characters are not side characters, they are not companion characters. They are main characters, full on protagonists, just like the host. They don't leave the party for the same reason the host's PC doesn't leave the party.
To play in multiplayer is to have multiple PCs, actual protagonist characters, not just to let your friends control your side characters, or a simple stand in (like a hireling would be).
To have someone join a run in progress, is to have a main character arrive late, but they're still a main character.
