This statement isn't correct. NPCs needs to see/hear you shooting or see dead body and use radio to rise settlement alarms. If you shoot from distance, there's not much noise which can be heard outside of buildings. And even then they stops pursuing you if you keep yourself some time (30 seconds) out of sight.
Personally I hope there will be at some future time added possibility to move bodies and really operate as stealth assassin. There's much what can be on foot improved, but for start it's good and I had allot fun while doing onfoot operations and learning how things works.
I've gotten a string of missions where I'm naughty. Them being green seems to help (yes, they like me and killing them sometimes seems to not matter...). But even if nobody sees you, you still get a bounty, which is
dumb.
But if the alarm is off, they're remarkably bad at coordinating. I pop a couple when I have to rush the power room, and the rest of the base is fine. Pistol kills seem to make minimal noise, doesn't usually pull anyone outside of a big room.
Just as long as I penetrate the alarm room FIRST, everything seems to go fine. An e-breach from a SRV left close to a door gets you into the building with minimal chance of scan, and if it's not restricted, you have unlimited time to find someone with access inside and be sneaky, then you rush the alarm and once it's down, "covert" missions become massacre missions.
I think maybe I won't take non-lethal missions.
Edit> The silliest thing is, I've gotten interdicted by something juicy on my way to a facility. So, I can get a ship bounty, auto-dock on their pad, turn in the bounty for money and rep, then... proceed to murder a bunch of people. This and picking missions based on type (covert_heist and covert_theft) and material reward for data that's almost impossible to get, has resulted in green massacre targets. Well, green before they go red.