1. We generally don't know as the general populace around here doesn't have the full stats. I would assume they work decently well, as the faction generic totems don't tend to have a massive amount of synergy with crews. Old Cranky, for example, will probably still fit in with Zipp's crew, doing what he has always done. Will he be better than Zipp's totem? Who knows.
2. To the best of my understanding, the new masters will not have upgrades with the emissaries. I could be wrong about this as I am just a guy on the forums. An emissary could still be hired with the generic upgrade, though, I would think.