Maybe the opacity was caused by restoration work painted over the original paint?

It could just be that those artists were using opaque paints. I think many modern synthetic organic pigments are transparent or semi transparent, even at high pigment concentrations. Maybe many older pigments are opaque? For example, genuine vermilion is one of the most opaque pigments. Genuine Naples Yellow, lead tin yellow, orpiment, and red lead are all listed as either opaque or semi opaque. Some red earths are also very opaque. Of course, there’s also many historical pigments that are transparent, and lead white is more transparent than titanium white.

I’m not sure if oil paints made with a roller mill have much more pigment than paint mulled by hand. I think roller mills may mostly just be better at fully and evenly dispersing the pigment in oil because of greater pressure. I’ve made oil paint by hand that had enough pigment to have similar tinting strength as paint from a tube, but this is easier with some pigments than with others.