Do what works for your body, but in terms of the science, there haven't been any studies to support it. You're on the right track with your thinking, in a way.
You're correct it takes time to digest the calories from a meal, but thats not why people say wait. usually waiting is just an issue of preference. Think about it. back when we were cavemen, our ancestors would have times of extreme famine, then have insane feasts (after a successful hunt for example) they eat as much as possible as quickly as possible. If the body was only able to process say 50 grams of protein in an hour and the rest wasted, we wouldn't be here today.
think about some great bb's like arnold and ronnie. their diets were insane, they ate more in one meal than a lot of people would eat in a day. if they had to only eat a certain number of calories, then wait for digestion, they would literally be up 24/7!
tldr- meal frequency does not have an effect on body weight. it may affect hunger levels or energy levels, but it won't effect how much weight you gain/lose.