One thing as a counterpoint - the larger a faction is, the more it presents a cross-section for attack.
You can put a faction into lockdown by attacking a ground installation and killing its skimmers. Systems with tiny populations that initially only had three, two, or even one faction present, are prime expansion targets. The low population also means that the influence levels in such systems can be bossed around very easily, which can put the faction into faction-wide states like lockdown, civil unrest, or war, blocking or overriding other states and negatively affecting markets and outfitting.
In other words, some factions might not want every system they're present in to be advertised by the game to all and sundry. Quality of life for you might not be quality of life for another group.
I wouldn't say that the devs don't want people to play with the BGS (it's the primary focus for my group); it's rather that it's a background simulation, not, to quote a dev, a "foreground simulation."
As for being friendly/allied with a faction and them not recognising you, one thing I've seen in the game is a system authority ship apologising after interdicting me, with text along the lines of "sorry, sir, I didn't realise it was you" -- the sysauth that interdicted me was for a faction I was 100% allied with. With regard to factions firing on their own, American police still shoot and kill American citizens, and pirates are, well... pirates.