First to briefly update you on both of my simple experiments, the one in which I simply added some oil to water and the other in which I added some molasses and oil to water. In both cases, the oil rose to the top of the mixture and stayed there as a film. This morning, after freezing overnight, the oil had congealed in both containers. I had not measured the amounts of oil but presumably the oils would weigh the same, or nearly the same, upon removal.
I also dissected your 4.7-ounce (133-gram) MM clone dough on paper. It includes 79.6 grams of flour, 40.6 grams of water, 0.48 grams of IDY (about 1/6 teaspoon), 1.19 grams of salt, 1.96 grams of oil (0.43 teaspoon, or a bit shy of 1/2 teaspoon), and 9.16 grams of molasses. As noted, the oil comes to almost one-half teaspoon. Maybe the other layer you saw is the yeast. Or it might be ash or barley malt or minerals or particles of bran in some form, possibly in combination.
At this point, I think I would just try to remove the oil or whatever it is at the top of your container and weigh it if that is possible. You might then let that material defrost to see if it has the original color of the oil you used. Depending on what you find, we can assess whether this type of experiment is worth pursuing further.