I'm not sure that's necessarily true. I'm personally of the opinion that The Hunt may well not be connected to the Thargoid mystery at all. I think that binary code seen in the David Braben interview / Alien interruption sequence was an Easter egg within a reveal (the reveal being the arrival of the Aliens but the Easter egg being something separate, perhaps tied into the story of The Missing).
I think those stories are connected.
FD seemed to indicate separate storylines for the game, which wouldn't necessarily overlap but now they seemed to change their minds, probably because they realised it'll be easier to follow for the players if they came up with a convoluted narrative which connects everything together more or less.
This way, they have the opportunity to attract people's attention to other parts of the game through the story which hopefully will have politics (powerplay), combat (obviously), exploration (far away places like the Rift) and all the other activities through various CGs created in the theme of a galactic narrative.
This is all speculation of course, we'll have to wait and see. Anyway, I'm pretty excited for the event starting this sunday, wherever that may lead to.