Processing level and calorie availability

I was just watching this youtube episode, where they mention how the processing level affects nutrient availability, especially calorie absorption.

For example, whole almonds may leave ~10-30% of calories "trapped" within the food matrix (later being fermented by our microbiota or lost in feces), while finely grinding almonds may enable almost all of its original calories to be absorbed.

I'm wondering if Cronometer provides a way to account for this. Claude says:

The Atwater system assumes a roughly constant digestibility across foods, but it doesn't account for food matrix effects. Whole nuts are the clearest counter-example — bomb calorimetry says the energy is there, and the macronutrient composition predicts ~170 kcal/oz for almonds, but human fecal-balance studies show ~20% of that energy is never actually absorbed because intracellular lipid stays trapped behind intact cell walls and ends up in the colon. So the Atwater factors systematically overestimate metabolisable energy for whole nuts, and increasingly so as the food becomes less processed.

It mentions the Beltsville studies as the "gold-standard human fecal-balance measurements", but still limited:

The USDA Beltsville group has been extending this work, but coverage is still patchy outside nuts.

This is obviously hard to account for, but I wonder if we could have, e.g., a discount factor to be applied to whole foods vs ground foods. Probably the place to start would be nuts, as previously mentioned.