I think the white skin for esp-added NPCs bug is still in.
I was wondering about that, because recently I read this post in the FOOK comments:
Not sure if this was brought up already, but there apparently seems to be a problem with the head color refusing to match up with the body color (screenshot). This only seems to affect NPC's modified by this mod. I'm not sure what causes it (I don't know as much about Fallout modding as I'd like to ), but if I transform FOOK.esm (master file) into an .esp (plugin file), this doesn't seem to happen.
It seems that user solved the problem by turning the esm into an esp, which funny enough would suggest the problem is the other way around this time.
But I haven't actually verified this myself, so take that with a grain of salt.
What would be more interesting to know if the navmesh issue is still present in esps.
Overall it would be best if we start verifying if any such problems exist and bring them up with Obsidian while they're still releasing patches for the game, instead of having to use workarounds like MasterUpdating again.