It didn’t get converted to ketones and expelled in your poop.

Your gut absorbed it. That is literally what digestive absorption is about. Expelling ketones is not digestive malabsorption.

There are many ways for food to not be 100% absorbed, which I think can most easily be demonstrated by eating a bag of nuts and waiting a day or two

I don't think it's unreasonable to think that different bodies absorb food in different ways (or proportions), particularly given what we've seen about the gut microbiome

Apparently even just changing the time of food intake can affect obesity (in rats) if this study is to be believed: https://pubmed.ncbi.nlm.nih.gov/22608008/

In response to, "but those are rats", I think it's a lot easier to cast doubt on "100% of food is always absorbed" vs "I don't think that always holds true"

I mean, heck: if there are no residual calories in human waste, how can it burn?

My original point: it's ok to assume you absorb 100%.

About the rat thing: the cico hypothesis point of view might look at whether meal timing affecting energy expenditure first, rather than assuming meal timing change digestive absorption.

There is not much point in getting in the weeds about how much you absorb, unless you're running trials on yourself like changing when you eat, or what you eat, and leaving all other things equal like calorie intake and expenditure.

The best dieting strategies I've seen track calories in and weight change. From their you derive calorie expenditure, and it really doesn't matter if you burned it or pooped it out, does it?