I think FD are very aware that we don't have the persistent NPCs that were put forward in the DDF, considering that for their events they've had to use "live-action" NPCs to simulate the role of persistent NPCs (such as Granger and his gang from when the first Thargoid Interceptor crash site was found).
Going on the DDF layouts, IIRC the tier 2 NPCs, which could interact with the CMDRs, were always going to be a weak link simply because CMDRs could kill them. This might work OK out in some corner of the bubble where a lone CMDR or a small group interacts with these Tier 2 NPCs as more than laughs (gaining valuable missions, etc. from them). But in areas with high CMDR traffic, where the odds are higher of finding CMDRs who simply kill every killable thing... I have serious doubt a Tier 2 persistent NPC would last more than a week.
This alone probably breaks the idea of persistent NPCs, who are widely known among CMDRs, and who may be eventually elevated to Tier 1 status.
The same idea when it comes to system population. Some small system has 1,300 population. If CMDRs could influence the system population, then many such smaller systems would have been mass-murdered to being zero-population, uninhabited wastelands within days or even hours of game launch.