For bounties perhaps, but this isn't how it worked in Horizons for notoriety. If you take a "kill civilians" mission in Horizons, you will not gain notoriety if your kills are tagged as mission targets. In EDO that's not the case. You can do a settlement purge and gain up to 3 notoriety points if the settlement isn't controlled by an anarchy faction. Basically it's as if you randomly went there and killed everyone. It's a more realistic way the law would be applied than how Horizons magically makes civilians not covered by the C&P system if they are mission targets, but definitely different than Horizons. It basically illustrated that C&P was designed for those who go off script on killing sprees. EDO seems to lasso those NPCs back into that system, ignoring what factions want, which is odd since "anarchy" is what a certain faction wants.
Well, I was just talking about getting a bounty if you commited a crime while in an anarchy system but close enough to a non anarchy asset. Although let's take a look at the notoriety thing because I'm certainly curious about the thinking behind some of it.
The problem seems to that they've gone back to an old mechanic of C&P for Odyssey. Once upon a time you had to complete a scan of any wanted ship (even if they were in the process of demanding cargo) or it would be counted as the same as shooting at a clean ship. The same thing actually applies to Odyssey, in that if you scan the target first before shooting them and if you do that, there's no bounty (against you) or notoriety.
Not sure why as this was pretty widely disliked back in early 2018, but that was probably more down to having to just watch a pirate in an Anaconda pounding a sys sec Eagle for a few seconds because to step in and shoot the obvious criminal before the scan completed would result in sys sec turning on you for your malicious assault.
Back to Odyssey however, I do wonder if you could end up with notoriety staying at 0 if you scanned every NPC before killing them in a settlement massacre. It would certainly be much reduced and you'd know you were killing an innocent before doing it (I don't care- I'm a mercenary with a job and ethics get in the way of my pay).