My non-scientific, and poorly researched understanding is that calories in/calories out is how you manage weight. But digestion itself is also a somewhat 'taxing' processes, and eating 3 square meals a day means you are pretty much constantly digesting food through out the day. For example, if you look into how type 2 diabetes works, your body basically can't produce enough insulin to process the glucose in your system (roughly), so you end up with high blood sugar. One way to deal with it is to reduce total calorie consumption, but it also feels like simply compressing your eating into a smaller window could have similar impacts (i.e. your average glucose levels throughout the day might be lower, even if you are eating a little more).

I wouldn't be surprised if there are other functions and processes in the body benefit (maybe kidneys and the liver benefit from some more 'downtime'). I am not a huge fan of the 'evolution' argument, but I assume our distant ancestors ate meals in somewhat sporadic schedules, so it would kinda make sense that our bodies are tuned to that cadence, as opposed to the constant supply of processed foods that we currently subsist on.