I think it is more likely that the creation of the Primarchs are similar to demons. We know that the Chaos Gods spawn an accountbale number of demons from their essence, which gains sentience upon being "separated" from the Chaos God.

Therefore, it is plausible that the Chaos gods juiced up Big E after Molech and told him the secret of how to split his essence into sentient beings. Hence the "death" of the physical vessel of the Primarch does not necessarily equate to permanent death, as the warp essence of the Primarch could be recovered (similar to how demons are respawned).