There's nothing to be surprised of: galnet plots have never had any correspondence with in game assets and or events - excluding CGs, the times when Drew Wagar was writing them to give hints about the rift and to hype his book, and when player-submitted galnets were a thing.
Drew Wagar's story - while extensive - didn't have that much in-game event to it either, considering it was spread over an entire year.
- there was a pair of competing CGs (not of great relevance to the plot, not particularly unusual for 2018-onwards Galnet)
- there were some Galnet stories related to out-of-game events (very normal)
- there was a large event at the end (the only really unusual bit, and possibly the bit Frontier might be looking to bring back for later stories)
- there were some in-game assets for players to discover (the more recent Far God storyline also had some of those)
- there was some close involvement with a couple of prominent player groups to make it look more interactive (more recently, the Gnosis)
It had the advantage over the current Galnet stories of being built around a strong and divisive protagonist, but I think is remembered as having much more in-game representation than it did.
Leave the minor faction in game and the BGS will take over: they cannot make the faction give out particular missions, they cannot make the faction control the market to, e.g., export religious pamphlets or whatever icon of Tothos, they cannot make the faction spawn security ships that behave like religious nutjobs rather than police officers, they cannot shutdown particular services of the stations controlled by the factions because, e.g., "material trading is immoral according to tothos!". The BGS does no exceptions - resistance is futile
They could do
all of that within current BGS capabilities.
1) There are a
few factions in the game which give out unique missions (or, at least, missions with unique text and in-game effect). The engineer invitation missions are the most obvious example which most players will actually have seen, but there are a few others as well.
2) Adding a new rare "icon of Tothos" and making it illegal in all non-Anarchy jurisdictions would make the station export it only when the Children controlled it.
They also have the regional goods (e.g. Reinforced Mounting Plate) which only appear in certain systems on a geographical basis, but are not rare goods, so that's also a possibility.
3) As an Anarchy faction it wouldn't generate system security anyway - but there's an existing "terrorist" NPC archetype that they could use instead. Scenarios, signal sources, etc. being restricted by BGS conditions is already there.
4) Continued shutdown of specific services is a little trickier, but Frontier have previously shut down certain services that a station would normally have without going through the BGS route, and there's already the long-standing feature where the opening or closing of a Black Market is determined by the type of faction in charge.
5) Specific stations (or entire systems) can be locked so that ownership cannot be changed through normal BGS methods either temporarily or permanently.
None of this is
free - new mission types or commodities or scenarios will require coding to add them, and lots of translation work for all the extra text they add to the game. So there's definitely a choice for Frontier whether they invest staff time in adding this sort of detail to the ongoing stories, or on developing the next game feature/bugfix. But that's a matter of prioritisation, not capability.
(Personally I think the game is at a stage where slower development in exchange for more detailed and better represented stories makes a lot of sense. On the other hand, given the "two years?!!?" reaction recently, I guess a lot of people would prefer quicker development and minimal-effort stories?)