Human enclaves outside the IoM exist because the things that go bump in the night missed them. Nothing human besides the IoM could deal with a proper Waagh! let alone something like the Beast, or a Black Crusade, or a Nid hive fleet, or a Necron tomb world's forces or well practically anything of note. The Tau are a significant interstellar polity and yet they've mostly survived by luck and not facing something serious - humanity being reduced to that is a huge loss.
Oh please,
the Imperium doesn't deal with proper Waaagh! or Black Crusades or Necron tomb worlds.
Parts of the Imperium do that, most of the time - you know, assets on the scale of a sector, like our conservative plans are aiming to take over. The Tau, meanwhile,
have beaten a Hive Fleet, countless Ork invasions, and three major Imperial campaigns, often while continuing to expand their empire. There's also the Interex, as we've been over before. It is simply false to claim that a star nation needs to be on the scale of the Imperium to endure the threats this galaxy has to offer; major campaigns like Black Crusades or Hive Fleet Behemoth are actually pretty rare, on the scale of the galaxy. Most of the fighting is the galactic equivalent of brushfire wars, the kind of single-planet conflicts that make for a decent Ciaphas Cain novel.
a) Chaos doesn't have that many fleets compared to the IoM - they're still capable of screwing large portions of the galaxy.
b) What place has Navigator houses? Terra. What place trains Astropaths and most psykers in general? Terra. The IoM might be a corrupt wreck but it is the top corrupt wreck in a galaxy that's actively hostile to human life for a reason. Well for a lot of reasons to be more precise. Surviving without the IoM's resources is more of a matter of luck than anything even without active hostility from the IoM (and there's little chance of that if we want to go full heretic).
a) Frankly, no, they're not. Chaos is overhyped. It rarely causes major wars outside of fleets roaming out from the Eye of Terror, and is otherwise limited to piratical raids and random Daemonic incursions when the stars align. That's not screwing over 'large portions of the galaxy'.
b) If we have ships, we have Navigators of our own, ergo we could found our own Navis Nobilite house if the need arose. Ditto Astropaths. The Imperium handles their training, yes, but they don't have that training on lockdown.
Like, you seem to be missing that
the Imperium does not survive with the Imperium's resources. Prior to Guilliman's return, the Imperium was
losing. It was a major element of the grimdark atmosphere that the Imperium was dying by inches, that each new catastrophe might be the straw that broke the camel's back, and a great part of the reason for that is the Imperium is riddled with tumourous inefficiencies and needless cruelties, which it embraces out of a misguided sense of necessity.
The Imperium is overwhelmed by the threats facing it in large part because it is wasteful, inefficient and self-sabotaging, and it persists largely because it is simply so massive that very few threats can do more than chip away at it. It is a fat, out of shape heavyweight boxer being beaten down by an endless succession of angry fourteen year olds.
For goodness sake, one of the most common wars that the Imperium fights is suppressing rebellions against its rule, because that rule is ridiculously oppressive and cruel! The amount of resources the Imperium wastes slapping band-aids on problems
it causes for itself is staggering, and this is not some tangential issue that can be fixed, this is the fundamental nature of the Imperium as a fascist polity. Fixing that requires such sweeping reforms that we'll be denounced as a heretic
anyway, so it'll be less painful to bite the bullet and go Defiant now, when we still have a grace period of nobody really knowing what the hell is happening on Sanguis.
Even without the power of Exaltation, we're going to be punching significantly above our weight class compared to the Imperium, simply by not being weighed down by all the crud that it embraces.