I don’t know in detail.
One problem evolution was trying to address was food scarcity, ranging from short term (e.g. failing to hunt or gather today, perhaps due to short term injury) to longer term (less food in winter, less food for a few years due to weather or a disease killing off some plants or animals or, but i doubt evolution specifically designed for dealing with longer term problems like a 10+ year famine). Another problem evolution deals with is variability in amount of physical exertion.
One potential reason that omega 6 fats (in higher concentrations) would cause weight gain is that your body is evolved to recognize those fats as a low quality food source that you’d only eat much if food was scarce, so it turns on some mechanisms for coping with food shortages like saving more energy. (why not save more energy all the time? presumably there’s a tradeoff involved with some downsides. maybe some energy saving options increase some sorts of damage to some of your cells.)
fight or flight responses might boost metabolism – conserving calories is a minor concern in dangerous situations. being scared for your life for a long time period might be a way to lose weight without exercising (given equal calories eaten).
Also the issue isn’t just metabolic rate (using energy up). It’s also digestion and extracting calories and other things from food (acquiring energy). How well we do that can be affected by lots of factors including what bacteria we have in our gut and whether the food is blended before eaten. Extracting part of a food, e.g. juicing, also affects digestion even if all your juice left out was fiber. There could also be bottlenecks like we can only digest something at a specific rate and if we eat too much of that food then more gets wasted (moves on to the next part of the digestion system before the current part does the most it can).