Commercially, thermophilic bacteria were added only to the pasteurized milk after discovering that the same make with raw and pasteurized milk produced the characteristic flavor in the raw but not the pasteurized.
A pure, traditional manchego is made with no added culture, and no lipase, and either rennet paste that has esterase, or a liquid rennet preserved from the spring lamb crop.
Nowadays, most manchego is pasteurized, so both lipase and thermophilic bacteria are added. Both are added as a way to develop flavor and for consistency.
Yes, raw milk in Spain used for manchego typically has enough bacteria to acidify and develop the appropriate flavor.
I make a cow milk cheese in the manner of manchego that has both lipase and LH and LA added, on a base of Danisco's 4001. Hard to get sheep's milk for me.