While hyperspace does tie together pretty well with the Warp, and the whole last half of the movie is essentially about "the warp leaking into reality", I always felt like the movie sort of stood on its own with its ideas. And the execution of most parts of the movie don't feel 40k either. A slightly grimmer general sci-fi look. Still, it's the kind of movie where if you put everyone in Imperial costume and threw some Aquilas around, the plot wouldn't be out of place at all. It'd just be a generally milder and slower building version of what generally happens in 40k
I'm kinda picturing it now. Adeptus Mechanicus Magos joins an Imperial Navy recovery squad to reclaim its lost research ship that suddenly re-materialized out of the Warp after being centuries of being missing. The ship is remarkably unchanged, most of it still functional and visibly uncorrupted by Chaos. But it's tainted in subtler ways. The Magos becomes obsessed with the Warp Drive as it has been changed by its time in the Warp, despite no log of the Geller Fields breaking down during the ship's absence. In the weird time of the Warp, it might have only been gone for a few days, yet if so, where is the crew?
The Magos, in studying the Warp Drive, becomes exposed to the Daemonic presence that crept into the ship through its Astropaths, and that wove its way into the ship's machine spirit, and becomes corrupted by it, a slave to its will. Lured by the dark knowledge of the Warp it offers him for his service, he begins prepping the ship for translation back into the Warp. The Imperial Navy troops start dying, the cruiser they arrived on gets destroyed when the Magos reactivates the ship's weapon systems so all they have left is their non-warp capable boarding craft. The Imperial officer in command decides that the whole ship and the Magos must be destroyed at any cost before it translates to the Warp. Final battle, Pyrrhic victory, yadda yadda yadda, roll credits.