Not having read the setting, nor being particularly interested in doing so I am going to play devils advocate here.
Personally I get a kick out of those folks who are seemingly obsessed with cannon and deride anyone who writes something they dont personally like.
Perhaps come down off of that pedestal and take a look at the material you appear to comparing this fanfic to.
40k fluff? Black library books? Sorry to say but its freshman level writing at its best. Little better in most cases then a random anime fanfic.
But his Stardust Empire idea simply does not fit with established 40k canon. End of. It cannot be saved.
Is this opinion or a fact?
Assume for a moment that you are correct in asserting the SE does not fit with established cannon.
My question then is quite simple: So what?
That entire treatise Foolamancer comes off as little more then a person putting anothers material down.