Well all I need to point out is that Jaques attempt to jump his station to Beagle Point and fail and end up at his current location was purely an FDEV implementation, nothing to do with players, I presume it was and still is part of the longer thargoid guardian story line.
Yes, obviously his current position was picked by Frontier. But given where it is, I suspect to
avoid potential interference with those stories, rather than to actively contribute to them. No Guardian ruins have been found within 10kLY of Colonia, and the closest Thargoids appear to be in the bubble.
But the fact he was making the jump at all was due to a Fuel Rat player-submitted CG, and the fact that he had UA interference was the actions of I think just two players. And even then, that could have been that - lots of things haven't caught on with the player base as much as Frontier expected - Jaques could have been repaired, then left there as a curiosity. That's hardly the sort of thing Frontier could plan for in advance, even if "we should have a deep space settlement someday" was on their list.
We also have no evidence that the deep-space permit sectors have anything to do with thargoids or guardians (the ones around Cone, Barnards and Regor clearly do, of course) - indeed, it's quite possible that Frontier has no idea what they're for yet, either: we're likely to reach the 2020 release with no permit region ever unlocked (6 years of game time), and could easily get through another 6 on just the ones near Sol. I'm pretty sure the more distant ones are just insurance for if the game lasts 20+ years and they need somewhere untouched to put a new storyline (at which point they would need a station or two adding on the borders anyway), rather than having all been carefully planned out pre-release.