It'd have to be done carefully to account for all the metaphysics and such, but it could be a very fruitful task.
Poked at it a bit, the main issue is deciding which setting trumps the other, and how. I can't see an easy way to do it without subordinating one setting to the other. For instance, the most obvious one is making 40k one of the 777,777 worlds, but that trivializes the 40k half of the setting. It basically has to be a setting merge. My take on it is basically making Throne the webway centre, and expanding the scale and role of this incredibly potent transport network in the universe. As a bastion of Old One tech, it basically denotes all Warp travel, and travelling anywhere in 40k without guidance from it one way or another is even harder than in default 40k. Every major faction barring the Necrons has a hold there somehow, with the Dark Eldar having succesfully set up Commoragh somehow as a pseudo-throne. Throne itself is basically a giant mess: because the Old One architecture is nigh impossible to meaningfully damage, everyone is forced to fight in an endless labyrinth of inactive inscrutable architecture. Other ideas I've thrown around are the Adeptus Custodes using the areas of Throne they control to flood the Astronomicom's light into the paths, with the Imperium using these guidelines to travel (an explanation to how the Astronomicon functions without blinding every psyker who looks towards Terra's general direction). Lots of stuff can be merged, like mixing the gods of the various species with unbound angels, and using soul powered martial arts as an explanation for how the Imperial Guard can fight Tyranids and not die instantly to poisons, for instance. There's also an opportunity to explore the less well known races. Like the Hrud. I want to run a Hrud quest now. Darn.
[the following is a rough board of ideas/notes. A lot is not written down.]
Cosmology: Chaos/Void, Throne, Material Realm
There are three realms, though in truth it would be more proper to say there are two and a half. The Material Realm, or "realspace" exists, and the Chaos Void impresses upon it. Throne is metaphorically the shadow cast upon the wall, sitting interposed and yet separate from the rest.
Throne is Malal? Yes. Throne is the webway and Commorragh as well. A Made up Chaos God, used as a foundation.
Automata: Beings of pure materium, without the influence of "souls" or whatnot. The C'tan are the main one, as are most AI. the Necrons became this. Megarachnids, Q'orl, Kroot and the like also count.
Mortals: All races born on the material realms, specifically those born naturally, without interference or the like. Crawling from the muck into ascendence. Humans, Tau, Demiurg, Nicassar, Stryxis, Tarellians, and so on.
Servants: Crafted by the elder ones, the Old Ones Who Were Gods, these races have a butt ton of advantages. Orks, Eldar, Hrud, Jokaero/Kinebrach, Ur-ghul and so on, all fall in this category. Servants grow consistently with power as they age. They freely pass between realms using the gifts and tools the old ones granted them. Neutral in balance between soul and shell.
Kindred: Warp creatures that exist, the "natives" of throne. Shifting between the real and unreal, skirting the edges and alleyways of Throne. Tyranids, Enslavers, and the like. These are defined by how they exist within, yet stand apart from, the warp. Khrave, Rak'gol, Thyrrus, and Laer count as this.
Angels: Ideas and Values bound into physical form. Each Angel is an ideal that finds form in the ashen fields between realms. Gods are a kind of angel, and are in many ways the ultimate form of these. Angels can be summoned much in the manner of devils, by binding their names onto a body cast of celestial ash. Angels reincarnate from a blank slate, growing with the tales of their exploits.
Daemons/Devils: the same kind of being, whether bound or unbound. Devils, being the bound form, Celestial Ash is required to make masks for them, as with masks come names, and with names come existence. Otherwise, Daemons are just masses of energy and stories unbound. These can coalesce under their own gravity into actual beings, especially if anchored by something. Daemon Princes and Greater Daemons, for instance, are created when the Daemon ascends their existence as mortals/servants or devils respectively, with their previously limited existence being coalesced as a star would be under the weight of their power. Every devil is ultimately always weaker than the daemon they are forged from. Devils rarely leave throne, as they greatly fear reverting to their primal state.
Inheritors: Those who have cast aside their past self in order to become something greater. Hero units are a great example, and have managed to "ascend", at least partially, their previous existence. There is a long path here, and the vast majority never make it. The God Emperor of Mankind is the example at the end of this path, and the Primarchs are all naturally on it, though some are further along than others. This path is exclusive to Throne, as Umbra are a requirement to proceed. Umbra technically fall here.
Factions in Throne
Eldar
- Drukhari
- Slave Species
- Harlequins
- Ynnari
Hrud Guilds
- Cult of Qah
- Stryxis Merchants
- Galg Mercenaries
- Slaugth Fleshcrafters
- Jokaero/Kinebranch
- Lacrymales
Imperial
- Custodes
- Ordo Terminus
- Mechanicus Luna
Chaos
- Laer Empire
- Rak'Gol
- Huron Blackheart
Wildcards
- Orks
- Genestealer Gangs
- Umbra
Wildlife
Of course, there is still the obvious problem of actually putting KSBD in. Fitting the Seven Black Emperors is especially awkward, and I'm tempted to cheat by saying they died a long time ago.