To me it sounds more like the typical FDev design decisions.
I find it rather difficult to distinguish between story elements, bugs, bad scripting and technical limitations.
What we have is official books that describe the Thargoids as hostile, very aggressive and generally not friendly.
Ok. I'll give you that. Although I'm not sure how much that means. We had story in the books in the original Elite about the Dredgers and colony ships but none were ever found.
We have GalNet news after GalNet news about Thargoid attacks, how Thargoids are "hostile" and a threat.
Galnet news? Since when has not the news been a tool of the government and other power players?
We have easily ignorable Thargoids USSs in the game.
We have in-game Thargoids that stay passive most of the time.
Yep. Leave them alone, they'll leave you alone.
We have a bug that resulted in Aegis looking like evil.
But was it really a bug? Or maybe it was by design. Look at the date that video was posted: 21/12/17. Now look at the date of the Patch note release: 25/01/18. More than a full month after the video was posted. Draw what conclusions you like but cover up is one of the possibilities.
We have really bad story telling timing with the INRA discoveries - unless the connection between Aegis and INRA is intended (something I don't think to be the case).
Are you really sure? Aegis and INRA both have (or had in the case of INRA) the same remit: To find ways to fight the Thargoids. So I'm inclined to think that they are connected. INRA got a bad rep. What better way to continue its work than to rename it and call it something else? Something that is not even an acronym.
We have previous games that apparently had bugs that prevented other story arcs to be playable resulting in the Alliance-Thargoid-Peace story to become part of the collective memory of those who played the previous games.
Again, the operative word is apparently. Since I don't work for FD, there is no way I can know, but Braben has had 20 years to get this story worked out.
We have the problem that after almost 3 years without aliens FDev can't simply let Thargoids destroy player ships left and right without really annoying a lot of players.
Really? You really think FD is that concerned about annoying people? How about all those that they annoyed the hell out of when their Pythons were nerfed? What about those that they annoyed when they reduced the ammo on heatsinks, or all those they annoyed when they made shield cells generate massive heat; in combination with a reduction of ammo a heatsink launcher can carry. From what I've seen, they don't seem that worried about annoying people.
The result of all this, in my opinion, is that the Thargoids make no sense.
Personally I try to remove everything that looks like it could be a bug or that is to complex from a story point of view from the Thargoid story arc. In a game that is extremely simple in it's concepts I don't expect that the story suddenly is very complex and nuanced.
Basically: Thargoids are evil and humanity is working together and Aegis are the good guys/gals.
If it turns out that the Thargoid story arc is different, then I'm very pleasantly surprised.
So what you seem to be saying in this last section, if something doesn't make sense to you, you tend to ignore it as a bug. Not a good idea, I think. Because some of it is not just buggy code. It's a grand design that you and I just can't see yet.