You don't have to go completely generic to avoid lawsuits, just get a little creative. A completely generic game that only exists as a legally-bulletproofed vessel for an IP mod isn't going to be a smash hit. Make a grimdark sci-fi setting that draws close parallels to the WH40K setting without using any copyrighted phrases or concepts, and you'll be fine.
For example, the space marines and the imperium of man in general-- they could be reskinned as "Imperial Knights", hulking biomodded supersoldiers wearing heavily armoured biosuits to prevent against the ever-prevalent biological hazards, radiation and industrial toxins of the setting. They could serve the God Computer, a sprawling life support machine slash supercomputer containing the digitized thought processes of the empire's founder. You could go the Asimov route with this and make him a great scientist rather than a godly warrior.
True to the grimdark setting, all human areas (even the dark insides of their spaceships) would be polluted to hell and back and swimming in background radiation from the various machines necessary for faster-than-light travel. The ordinary human is sickly and has most of their body cybernetically replaced to survive their harsh environment, but the Imperial Knights are more or less "pure" humans enhanced by genetic modifications and unobtrusive internal cybernetics.
This is where the geneseed mechanic comes in. Imperial Knights, like space marines, live in isolated "monasteries" with powerful radiation shields and atmospheric filtering in stark cotnrast to the rest of the setting because if they lose too much DNA integrity, aka geneseed purity, they become more "disentangled" and sensitive to the influences of Subspace, aka the Warp. When an individual becomes disentangled they gain powerful extradimensional abilities at the cost of monstrous biomechanical mutations as their intelligent cybernetics and biomods turn rampant and meld with their body. To counteract this, the Imperial Knights store their "backup organs" in Legacy Chambers, which are cooled and atmosphere controlled even beyond the normal for their compounds. Backup organs are basically geneseeds-- it's a symbiotic organism that stores a complete human genome made from the combined DNA of all its previous owners, and it releases the required mutagens, steroids and developmental drugs and hormones required to elevate the Knights above normal humanity.
Of course, regular humans can become disentangled too, but their DNA is already so damaged by the conditions of the setting that it's difficult for them unless they really try. They can purposefully disentangle themselves by performing occult rituals or constructing devices to weaken the barriers between regular space and Subspace. People who are already disentangled act as local conduits and may cause corruption in those around them, which is dangerous if they hide their true nature. Subspace denizens could be powerful energy beings overseeing the twisted biomechanical hordes of corrupted humans.
To solve the founding chapter problems, Knights can be split into a certain amount of original Orders, with every subsequent group being a "Sanctioned Splinter", which is an order created from an existing order for the same reasons new chapters are founded. And naturally there are "Renegade Splinters" which act as chaos space marines, split off from their originator Order due to ideological differences, infighting, coups, unorthodox/inhumane practices or Subspace corruption.
For the other aliens, it's just recognizing the tropes that make them the way they are. Orks are violent scavengers capable of making functional machinery out of garbage-- they could be replaced with a diminituve reptilian or avian race to play on this, like velociraptors in space. Eldar are the condescending forerunners who look down on everyone despite being reduced to near-irrelevance after being FUBAR'd by their own superior technology-- in this case, they could be a race of humanoids with advanced, almost-magical technology that allows them to more-or-less safely harness Subspace energy... except for that one time where they catastrophically destroyed almost their entire empire. Tyranids are a pretty typical devourer-alien, so they can be replaced easily by a reskin without any fear of litigation.
All of this not only makes an easy framework for any future WH40K mod, it would also easily stand on its own as a WH40K-inspired setting if it was fleshed out a bit more. Also, sorry for the wall of text. At least I formatted it.
These are all just ideas I'm tossing out there, and I'm sure there are better worldbuilders than me on this forum. The point is, be inspired by Warhammer 40K, but make this your own game. Let the mods come sooner or later, but don't rely on them to make your game great.
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Topic: Chapter Master - In the name of the Emperor! (Read 809980 times)