Okay, here me out. Since you all say that Mechanicum fits easily with the new fluff (Cote and Seripion for example) work with me here. The description given of the "shard" of the Void Dragon was basically something that was powerful enough even severely weakened to challenge the most powerful psyker in the known universe. Not only could it challenge the Emperor, but he was unable to destroy this "shard." Turning lemons into lemonade, he constructs an elaborate prison to use the creatures know-how to inspire the Mars engineers to build him an industrial machine that could pretty much arm and transport his armies. That is ONE FREAKING SHARD.
I understand what you're saying, you have said the same for your last couple of posts and we have replied accordingly.
Yes, the Dragon of Mars is only one shard of several. Yes, it was a challenge for the Emperor to defeat. Yes, it indirectly helped to create the Mechanicum and thus the Imperium. No, the Emperor wasn't able to destory it, only imprison it. We acknowledge that.
But as you have acknowledged, the shards are still beings of "near-unlimited power", and are only limited by their "imagination" and "glittering memories". For all we know, the shards have the potential to wield just as much power as their consummate forebears, but are limited by their fractured minds and the inability to glean the memories and awareness they possessed before they were shattered. The shards are also presumably just as impossible to utterly eradicate as their predecessors were, so its no wonder the Emperor was unable to destroy the Dragon of Mars.
I see no issue (big or small) with the narrative at all: A shard finds its way to Terra, where it was fought and subdued by the Emperor. The Emperor found it impossible to destroy (which fits the new lore) so instead imprisoned it under the sands of Mars, with the long-term intention of fostering the Mechanicum. The shard (still a being of "near-unlimited power" remember) was then able to subtlety influence the human colonists on Mars to develop their knowledge and appriciation of technology, eventually leading to the development of the Mechanicum. What part of that poses a problem exactly?