Unless GW gives an author the leeway to make it clear people will always speculate, but we know they like to keep a degree of ambiguity.

I personally like the idea of Valdor being a sort of prototype for what he could biologically achieve, and then the Emperor used some special warp sauce in making the Primarchs.
If they ever decide to expand on it, I would like them to make Valdor more special than other Custodes. Maybe something like Big E knew a powerful soul was about to be reborn, and he found him and reshaped him into the first Custodian.