I'm wondering if everything that happened in Elite 3 is still canon ? That seems like should be a good source of Thargoid lore.
As far as I know Thargoids communicated with the human commander, and even (possibly) gave him a ship as a reward. Also the Alliance back then was more or less friendly to the Thargoids, although it's undestandable why they'd hate the Empire and Federation.
No, it isn't.
Frontier: First Encounters (FFE), number 3 in the Elite series, had a Story the player was to follow. It was intended that the Story have two possible endings, based on player choice: become friendly with and help the Thargoids (and they give you a Thargoid scout ship to fly as a reward and usher in a new golden age of peaceful coexistence), or side with the INRA and destroy the Thargoid remnant fleet. Due to bugs (FFE was notorious for being bug-riddled) the player couldn't actually complete that second option. But FD have said that the second version of the story is the canonical version of events: from the Thargoid point of view, humans tried to wipe the Thargoids out a second time with mycoid. They're still here, so it looks like they failed. I doubt the Thargoids believe in "third time lucky".
In ED, the Alliance has joined the Feds and Imps to form AEGIS, a tri-party anti-Thargoid taskforce. So they are not (currently) on good terms with the Thargoids.