I agree: Chaos is going to counter them hard.
There is a certain (technically, a multi-author fanfic) scenario that puts the Culture (from Iain M Banks) against the Warhammer 40k Universe, exploring it in rather significant detail.
The Culture is, at any point it wishes to be, utterly superior to Humanity during the Dark Age of Technology. And significantly less grimdark. Primarily because it is a bit like if Humanity got through the Dark Age of Technology and came out the other side folicking through the fields with a benevolent group of AI.
Why do I bring this up? Because The Culture in that context is essentially the "best case scenario" equivalent for Humanity during the Dark Age of Technology. DAoT Humanity isn't going to be able to perform better than The Culture, which is further along the tech curve.
The Orcs? Not a problem. Nekrons? Can be worked around. Tau? Eh, we can make friends. Tyranids? That is very clearly a homogenizing swarm, kill it with gridfire, but otherwise it can be contained. Psykers? What the hell is going on? Chaos? That, my friends, is a full on outside context problem. To quote Banks: An Outside Context Problem is the sort of thing most civilizations encounter just once, and which they tend to encounter rather in the same way a sentence encounters a full stop.
They identify it as the single biggest threat to them in the galaxy and quite possibly the only thing that has the potential to destroy them utterly. Their technology is only of questionable use against Chaos, as Warp Storms don't care too much about things like physics, but Chaos may be able to repurpose their tech. Significant effort is put forward to ensuring that no part of their technology can be recovered if chaos contamination is detected, to the point of self destruction. It is enough of a problem that they determine that the risk is too great for Culture ships to engage Chaos directly, and a large portion of their interactions with the Imperium form there on out is attempting to figure out how the Imperium manages to deal with Chaos.
DAoT Humanity faces the same issue, but is missing many of the tools, and there is no Imperium to draw from in order to mount a resistance before major losses begin to occur. Chaos doesn't need to win, they just need to corrupt, and DAoT Humanity is going to be very prone to it.
This all but ensures that DAoT tech will fall into the hands of Chaos. And once that happens, DAoT Humanity is fundamentally doomed.