Very interesting project, reminds me of the early days when GW blurred the lines of the fantasy and scifi universes.
Exactly; back in the day, you could actually equip your Chaos warriors with Bolters and Chainswords and the like (in books like The Lost and the Damned, and Slaves to Darkness). In the earlier (sadly reconned into oblivion) fluff, the WHFB world was located somewhere in a pocket in the Eye of Terror, the Old Ones were the same Old Ones as those in the 40K universe and the Slann connected both settings (just like the Chaos gods and (almost) all the races in the games).
I'm pretty sure that 40K evolved from WHFB when they expanded the setting from a bog standard fantasy world into a bog standard fantasy world with a whole galaxy around it. 40K/RT filled in the gaps (or void, if you will
) around that bog standard fantasy world, by directly exporting and expanding all themes and races into space.
Later, GW severed all links between the two settings, but even as late as the Albion Summer Campaign in the late nineties (or was it early 2000s?), there were 40K links in WHFB. For instance, in that campaign, players could win awards such as Boltpistols and Powerfists!
I actually like those links between the systems, so I have a Chaos Sorceror kicking around somewhere, with a holstered Boltgun hanging form the pommel of his horse...