The instructions from my densitometer tell to put the negative emulsion-up when reading. I believe it relates more to the definition of "diffuse" reading, and affects the scattering of light, more of which is then collected by the photocell if the scattering occurs up into space, than into the base and light-piped elsewhere.

I figure a blue filter would give different readings than the visual filter, and the difference may imply "density" as might be attributed to stain. Don't know that it would accurately measure it, but at least it would detect yellow.