It seems that nuts are harder to digest than we thought [0], and thus our bodies do not extract as much energy from them.

Also, composition of gut microbiota seems to have an effect on metabolism and obesity, at least in mice; that should not be surprising, given that gut microbiota "predigests" some nutrients for us. [1]

[0] https://thecounter.org/scientists-calorie-counts-usda-kind/

[1] https://www.ncbi.nlm.nih.gov/books/NBK154098/