This thread is all about the what ifs about 40k and ides about answers to age old questions. Ill start, what if the emperor is really the deciever?
Well, in all likelihood it would confirm that someone else was on the Golden Throne and being used as a psychic conduit, most likely Horus or another primarch. In addition to this it would also likely have altered the entire role of the Imperium, turning it into a more expansive force with a greater emphasis upon hunting down certain worlds. Those which held the C'Tan or sleeping necrons would likely have been obliterated to prevent others from competing with his power, or enslaved to augment his forces. This is all without mentioning a more dominant role of the Mechanicus as, in all likelihood taking a role equal to that of the astartes in terms of frontline importance, and artificial intelligence becoming a goal within the organisation rather than a taboo.
If its a clone of the emperor than his almighty power would lead him to the true emperor to carry out his task
The biological body would be flawed and not possessing of a particularly incredible strength. The Emperor's real power comes from his soul, therefore a clone of the Emperor wouldn't be anywhere near as dangerous. It'd probably get killed for ultra heresy, many Chapters and Ecclesiarchy Forces will come after Bile, too many for him to escape from before being purged.
Ah! But the Thorians may come after the Clone to claim the body so the Emperor can reincarnate into it. So what if Bile made two clones of the Emperor, one of which falls into Thorian hands and the Emperor uses the body, whilst the other Bile turns into a Daemon Prince? So what then?