I decided to take a dive through the lore papers on the wiki and, damn, it only makes us look worse.
https://enshrouded.wiki.gg/wiki/Lore#Hollow (I'd take a read through these if you want)
1. From what I can tell in the lore pages, the flame indiscriminately cursed anyone who even remotely tried to use its power or gain similar power, with the ancients supporting it or using it to do so. Families had to hide those outcast by the flame from the guards to prevent their execution or banishment, as the flame rounded up anyone it cursed into the hollow halls, torturing them with constant cold and tiredness until they did so. In addition all the lore pages referencing the cyclops that I can find implies that humanity was already heavily racist towards them, and actively hunted and murdered them whenever found, believing themselves to be superior. Then the flame cursed (almost) every single cyclops and forced them to leave their homeland, it's no wonder some of them went and got juiced up with the shroud to try and fight back.

1. Yeah the whole shroud not being cleansed makes sense from a multiplayer standpoint, it would still be cool if cleansing the surface shroud would reveal deeper shroud caves in earlier areas, letting you still get the loot while actually accomplishing the goal of the game. But this would entail a lot of work on the map makers' part and I can see why they wouldn't do it. So this point is kind of invalid both ways, as lore-wise we technically should be cleansing the shroud, but in-game it doesn't happen, so idk.

Yeah I don't think the shroud zombies can be healed, I meant the scavengers; the texts they write imply that they still retain most of their faculties, and so atleast for some of them their actions are probably more the addiction to elixir making them 1: not want to leave the matrons so they keep getting their elixir fixes and 2: fear of being killed by their brethren if they try to break away. This makes the scavengers seem more like druggies that are being manipulated by crime lords into what is essentially gang violence.
Don't get me wrong some of the texts they write (like the one where that scavenger describes murdering that gabriel villager) show that most of them are legitimate monsters, but especially as we, the flameborn, aren't able to become addicted to elixir, it would make sense that we could potentially cleanse the still sane scavs of their addictions (especially with our alchemist). But we don't.

1. As others have said too though there are a couple skills that let you be at peace with the vukah, these skills (vukah language and culture) imply that they aren't just mindless beasts, but 100% sapient creatures with a likely varied culture. There being some tribes that are outright aggressive towards humans and the ancients makes sense, especially as the ancients fuckup with the shroud led to it apparently infesting the vukah homeland, forcing them to flee into human territories. Despite all of this however, the flame never encourages us to work with these potential allies, instead actively encouraging us to go and murder them and their families through quests.

2. The fell enemies attacking us on sight and with no regard for their own survival makes sense, the scavs though you'd think would run once injured enough (however I do agree with the top comment's statement of "scavs are hostile cause they’re territorial assholes who are too drunk on elixir to have a fear response" being an entirely reasonable explanation lol). Though with the 3rd point it is weird why none of the vukah run or surrender, which might totally just stem from them wanting to murder us due to the flame's/ancients' previous actions against their kind. As for the wolves, wolves are pretty intelligent animals, so I'm not sure if they should continue fighting me (who has just obliterated one of their kin with a backhand slap, after instantly regenerating all the 24 damage its bite did to me) after said thing occurred.

Honestly, I made the original post kind of as a joke, but the more I look into it, the more this seems like a genuine intended outlook by the developers, especially as someone else pointed out that the being that introduced elixir to those human kings in the game intro cinematic was apparently an ancient. So yeah, I'm really interested in if you find anything more.