I looked through the rules and I have not been able to find a definitive answer. I know as the owner of an npc I can assign tags/fitouts, create squads, have them pickup/drop their equipped items and do various other things. What can someone do if they are assigned as the manager or supervisor of an npc?
Supervisors can at least party/squad them, and they can also command -> Pickup/Drop Fitout. Unfortunately due to Tags being Owner-Only, Owners are the only ones that can actually set the fitout tags, but once they're set Sups and above can issue the command to pickup/drop&pickup etc.
Managers can definitely assign skillpoints to NPCs as well as doing everything Sups can do.
Is there a particular reason supervisors are allowed to order an npc to pick up/drop fitouts? I can understand commanders could do that because they would be managing the squads but supervisors are there to use the squad, not manage it so there must be a reason.
Tactical switching of weaponry is a good reason for having sups be able to drop and pickup. Having two fitouts placed on a single NPC squad would mean they can switch between both, but making it so a manager has to do it would put you at a serious disadvantage if said manager wasn't around.
It also bears mentioning that Sups and above can use the NPC Control function to manually equip items to the NPCs. Occasionally people "find" better gear that might benefit the NPC, or occasionally you may want to equip a specific set of Custom Items (which you cannot do easily through Fitouts), or occasionally you get assigned some NPCs that have no fitouts assigned.