Chaos got pretty much everything right.
Which invokes the question why didn't the great Four make sure the Eisenstein got lost in the Warp permanently or at the very least make sure its journey either drags out to a millenium or make sure it pops out back where it started or far, far away from where it did, which is right in the path of the Phalanx. I figure only a being of the Emperor's power might have caused this, especially given how he calmed the path for Thor during the age of Apostasy, but this would, again, require his foreknowledge of the Heresy.
his guy's cosmic power was staggering - enough to go up against the Four Gods of Chaos and win (to a certain extent; it is often mentioned that he "stole" power from the Chaos Gods). The Chaos Gods can grant their followers power - it makes sense that the Emperor can do the same (to a more limited extent, under certain circumstances).
All the more reason for him to know what was going on. He couldn't have inspired a saint with visions, inspiration and protection blindly unless he a) had some idea of what was going on and b) had some mental or warp presence in the region.
I don't know whether the Emperor just had really good multitasking skills or there are parts of his power controlled by his subconscience but having faith open a conduit to his power somehow doesn't make as much sense to me when he's alive and walking around as it does when he's destroyed, bound to a giant psyk-conduit and has his full (un)divided attention on managing his domain. Not to mention that the region of space where he inspired a saint was obscured from the rest of the galaxy by warp storms, which also brings with itself additional question of how and why everything happened the way it did.
He loved his sons to a fault, and the fault was believing too much of them.
With all that love he could at least have dropped a hint of why he was retiring to his most beloved son, a warrior without peer, a diplomat supreme even if he stayed silent on his motivations to everyone else.
Also I feel that his Imperial Truth is another reason why he shouldn't care about indulging the growing cult with evidence of his divinity through inspiring one remembrancer unless his powers are so great they just automatically start shedding around whenever someone asks for them with enough faith.