While the research DOES say that some food are digested later in the tract thus the available energy is not fully released by the body, but rather used by the gut microbiome, it does say nothing about quantity. Ultimately you gain weight because you eat more than your body require to maintain weight, and store the excess as fat. I *did* live through that going from ~84 kg (my "normal" weight without too much fat) to ~96 kg (main reason was me eating too much and stopping doing sport due to depression). Now that I am doing sport (not that much 4 days a week and 30-40 minutes daily maximum - some week I even only go once per week) again and slightly changed diet to limit my calorie intake, paying attention to not go above board, especially stopping ALL soda , guess what ? I lost 5 Kg in 6 Months. I am below 91 Kg now.
Ultimately while there are SOME subtlety about calorie and how they are absorbed "Eat less, move more" is ultimately correct. For the average person No metabolism problem whatsoever will force you to eat the equivalent of 3000 cal per day. Exercise is an issue, I saw myself how difficult it is to pick up, but watching calorie in , yes that's an issue most people ignore and gain loooooot of weight from.