Sorry for the wall of text in advance
The Orks infight constantly and only gain strength when a powerful non-Ork force gets rolling. They're like hornets, they're dangerous and wildly aggressive but if kept at a distance won't cause you problems. The Beast doesn't occur in a vacuum, The Beast was the result of The Emperor raising a galactic empire with massive resources. No Imperium no Beast.
The Tyranids are literally only in the Milky Way because of a long chain of events that wouldn't have happened without The Emperor doing his shenanigans. No Emperor fuckery then no Great Crusade. No Great Crusade then no Horus Heresy. No Horus Heresy then no Pharos Incident. No Pharos Incident then no Tyranids attracted to the Milky Way.
As for the Necrons most of them are wildly isolationist and if left to their own devices won't fuck with you. Sure they'll genocide the planet they're on when they wake up but most of them stop at that and are content to just link up with other dynasty aligned tomb worlds. The only reason Necrons are so problematic again loops back to the butterfly effect with the Tyranids. If the Tyranids don't start visiting the Milky Way The Silent King continues to fuck off and not start uniting Necrons and forming Pariah Nexuses. This shit is all connected back to The Emperors hubris.
Even Chaos which is only such a big problem because The Emperors plans gave them half a big ass galactic empire in manpower with demigod that are able to keep legions of transhumans loyal and ready to fight. Chaos without realspace followers is by its nature a temporary problem. Daemons no matter how intense the summoning ritual peter out super quickly on a galactic scale. Their legions of followers willing to fuck shit up in a long term manner is a direct result of The Emperors hubris.
As for the C'tan it's indisputable that almost everyone including non-humans is better off for The Emperor suplexing the Void Dragon, but that doesn't mean his plans didn't massively fuck up the universe. Under our current knowledge it was completely possible for The Emperor to protect humanity from existential threats while they evolved naturally. He could have beat the Void Dragon and left well enough alone.
All of these problems are a direct result of The Emperors plans fucking the galaxy. The only current factions that remain relatively unchanged and at their current power level without The Emperor shotgunning humanities progression is the Tau and every variation of Eldar. In universe there's a completely legitimate argument to be made that if humanity had been given the chance and time to develop naturally that 40k instead of being grimdark could be a pretty nice place to live. Maybe not too but the current setting is an abyssmal failure for the most part because of The Emperors meddling. Given a chance to redo for humanities best interest about the best thing you could do is delete The Emperor from the setting immediately after he beat the Void Dragon.