The thousands of players that participated in the war outside of hip will not be accounted for.
That's true, but preserving progress within a particular state wouldn't change that in most cases because the progress is far too slow anyway. The vast majority of systems threatened or controlled by the Thargoids don't even have a single ~2% tick of progress showing yet. Letting them pile up progress for a few weeks won't help.
It'd need progress to not be reset at all even when the system changes state - so Alert, through Invasion, through to Control, and then six months later the system is finally recaptured because "one Thargoid a week" finally built up to enough. And then it's in the middle of Thargoid territory so they probably invade it again a few weeks later and the bar is ... er ... reset. That sort of sparsely-contested system has problems unrelated to the reset for maintaining it, and the effort is probably "futile heroic gesture suitable for 19th century state war poet" regardless.
At least with this narrative, fdev can alter the thresholds as their narrative requires to lead us to the outcome they desire
They can, but other than in extremely broad terms it probably doesn't help their narrative if they do, and they probably don't have any strong opinions on which specific systems should survive.
They can't make us defend any specific system no matter how easy it is (and the thresholds have to be low enough that they can't absolutely make us fail to defend a specific system either). But equally, the bubble is really big even after the Thargoids take a noticeable chunk out of it, so it doesn't really matter if the Thargoids eat 10% or 90% of the bubble in terms of finding a system with suitable properties for the next plot event.
There might well be a "victory at HIP 23716 celebrated" Galnet article ready to go - but the name will have been filled in later, etc.