I've been experiencing non-hostility from NPCs, like from caesar when I killed everyone in his tent.. he just sat there. There are other examples but I don't feel like typing them all out.

Were you doing all the killing while sneaking? I noticed that once, on Fortification Hill, even with Boone tagging along, when I killed all the Legion peons on the way to Caesar while crouched/sneaking, I guess there weren't any witnesses left to my carnage so I hadn't reached Vilified again/Failed the quest yet. I might have been able to leave Boone outside the tent or the area before it, and gone in and talked to Caesar, but I wasn't in a talking mood.

Then again, if I had tried, maybe they would've attacked anyway. I didn't actually test it.

If you are not detected, you will not gain (or lose) faction rep for killing or crimes you commit.

I was detected, I burst into his tent with a ballistic fist and E-DE. I killed lucius infront of him. This has happened with NCR people too, I would kill 8/10 NCR guys, and the last two would be like, "patrolling the mojave makes me really sad."

Close combat weapon / silent weapon plus companion kill..

I've just verified this.

Arm a melee or another silent weapon, stand up in the open and allow a companion to kill the target.
No sneaking or hidden status is needed you will lose no reputation at all.
If however you started with or have currently equiped a "loud" weapon;
Faction reputation loss will still take place despite who actually delivered the killing blow.

The only other ways to do this is to use a silenced weapon while sneaking and making the kill yourself.
Or using a loud gun, but have no companions and not be spotted, ( however allies of the target still turn hostile for a bit ).

However yours may be a bug, I'll just check.

Edit: Not getting the same non hostile with NCR.
Did you one shot and holster your weapon by chance?

I'm telling you, it must be a bug. Because aside from not attacking me to start with, upon exiting vats hostile NPCs will stop attaching me. Their little AI fists will be raised in anger, but they will not move.