Here is the thing. The Imperium of Man does not really understand they own tech fully. They have a vague idea of how things work. But unlike them The Federation not only knows their own tech fully but can back engineer tech millions of years old. Points at back engineered Iconian tech. 40K techonbabble is like Starfleet when they are fully drunk and going off only 1 hours sleep after 72 hours of working straight. They aren't in the same technobabble league and never have been.
The Human Federation thingy from the WH age of Strife thought they understood their tech fully, before Warp fuckery happened.
Same goes for the Elder and the Old ones.
Also, what the Mechanicus "vaguely understands" is orders of magnitude more powerful ancient tech that outclasses anything in Trek.
Also all of that superstition exists with very good reason.
First off, some areas of scientific inquiry lead to potential corruption or the creation of Abominable Intelligences, which either understand chaos and decide that the only way to stop it is to destroy all sentient organics, or like in the case of the Men Of Iron get corrupted by chaos.
Faith in Warhammer is literally one of the strongest weapons against Chaos, and the happy go lucky Fed troglodytes have zero protection against it.
Their society is very similar to both the original Earth Federation and what Emps tried to achieve with the Imperial creed.
Also, it is strongly implied that much of the tech in Warhammer had machine spirits that act as rudimentary A.I. and thet were either A.I. or something else, they sort of want to be worshipped.
And as I said there is the aspect of the Warp influencing reality as a whole.
For all the cheerleading about the Feds, they have routinely been brought low by exceedingly incompetent and stupid enemies who did not have their alleged treknobabel abilities and the majority of the "bounce a greviton particle beam off the main deflector dish" stunts were never used again.
Trek loses, hard.
This will not be a single enemy, millions of them will fall to Slaanesh or Khorne or Tzeentch in a matter of days, and they will be raided by everyone from the Dark Eldar to Orks and the Imperium.
Their best scientists will become obsessed with new and dangerous experiments.
Their best officers will turn so bloodthirsty as to make Klingons look like pacifists.
Their political leadership shall become corrupted by the thirst for power.
Furthermore, Chaos does not act directly.
Failbadon not withstanding, chaos uses corruption, persuasion and trickery and infiltration to weaken it's enemies.
At least until Tzeentch gets involved.
Slaanesh is the one they should really be worried about, but I think that all the mad scientist and artsy types in the Federation will be split evenly among Slaanesh and Teeentch.
Tzeentch will take the shxeming politicians, Slaanesh the salf-aggrendizing ones.
Also, Warhammer is no stranger to time travel, I fact that played a part in the birth of Slaanesh and the scattering of the Primarchs.
Also, precognition plays a huge role in Warhammer.