Needs a bit more detail, there’s two major ways this can go, which differ wildly in implementation difficulty.
- NPCs have “affinity” for certain tasks, and perform them when those tasks are available.
i.e. Lumberjacks will always go chop down trees and plane wood if possible, electronics crafters will always prefer to build electronics, etc.
The PC still generates the list of tasks everyone pulls from.
- NPCs left to their own devices will try and build and improve a settlement.
This is much more difficult to do.
Likely commands from the player would override NPC decisions.
This is more about having “player isn’t near” type combat at all than anything else.
I think this is in?
This is the only suggestion here that’s not a week+ of work 
No problem with this in principle, but it needs to have a system in place for “stuff NPCs do when the player isn’t around” which doesn’t currently exist, and somewhat careful balancing so that you don’t just leave for a week and come back to end-game skilled NPCs. Subtext here is that the player at least has to meet their physical needs while studying, but currently NPCs don’t even have to eat.
Can you expand on this? Why do you need to constantly tell them to guard/follow?
Yea that’s a pretty amazing idea. Thinking about bolting it on to the advanced inventory code doesn’t make me happy, but it would be an amazing feature. For picking things up though, using “look around” to designate items for pickup would be pretty boss and would be much less complicated. Hrm, that would be doable even if you don’t have companions, just pre-select a bunch of items until it says your inventory will be full, then hit go and have it auto-navigate you to all of the locations to pick them up,