Personally, I find the fact they are scooping up manned escape pods a bit disturbing. Sure they could be rescuing them, but as of yet I haven't seen a single report where the pods have shown up at stations or dropped off in shipping lanes for rescue. I'm sure they are capable of finding human stations and nudging manned escape pods through the mailslot but they haven't appeared to do so yet
I've made it one of my missions to rescue manned pods before they get scooped up.
Given they've altered the lore as needed since ED is more of a reboot than an actual sequel, I'm inclined to believe the Thargoids aren't being friendly. They do get angry over escape pods, and will also collect them if you drop one. Their reaction is very similar to how they act in relation to Meta-Alloys.
Either they're collecting the pods and making Solyent Green, or they're harvesting the genetic materials for some unknown purpose. I doubt we'll see any of those people again. Lets also not forget that Thargoid technology disables Human technology and the interior of their ships are quite cold. That alone implies any collected pods will likely leave the occupants dead in short order. Then of course there are the Guardians who were likely wiped out by the Thargoids. They go berzerk when you have Guardian tech on board your ship, which confirms a connection.
As far as strictly adhering to lore, I look at it this way. Given the events of FFE, the Thargoids could easily have contacted humanity and proposed a armistice, or asked us to leave their barnacle sights alone. They've communicated in the past and actively chose not to this time around. They also chose to hide in the shadows and then launch surprise attacks without any dialogue. To me, that speaks volumes. Just because they're ignoring us unless we do certain things, or are carrying specific items, does not make them friendly, or even neutral. It simply means they don't consider us a serious threat, or particularly worth talking to. Given what we do to each other, can you blame them?
"We don't know much about aliens, but we know about humans. If you look at history, contact between humans and less intelligent organisms have often been disastrous from their point of view, and encounters between civilizations with advanced versus primitive technologies have gone badly for the less advanced. A civilization reading one of our messages could be billions of years ahead of us. If so, they will be vastly more powerful, and may not see us as any more valuable than we see bacteria." - Stephen Hawking
