There was no formal definition of race at the time, but whites of the Middle Ages still discriminated based on skin color and religious beliefs, which set the foundations for all-types of otherizing mechanisms that would develop into race as a fluid social construct and give us such historical beauties as the Spanish Inquisition and the Atlantic Slave trade.
Having darker skin was considered sinful. Ever heard of the curse of Ham/Canaan? Early depictions of Satan describe him as being dark-skinned.
The expulsion of Moors from the Iberian Penisula and Jews from Spain started as a result of mere geographic conquest but fully developed into racial discrimination after religious persecution. Lack of fealty to Christianity made you "impure" and the dichotomy grew even broader from there.
So, yeah, technically you're correct that it wasn't the original intention behind the conception, but that's just you being a Technical Genius on the matter. "Genius" being utilized with a strong sense of irony here. You're being pedantic and completely missing the meaning behind words. That, or you're one of those "Dark Enlightenment" advocates, in which case, let me get my ignore list ready.
The light/dark dichotomy in Christianity has been more than a mere metaphorical staple, but an otherizing tool since pretty much the very beginning and the two co-evolved over the centuries.