No, the MC's forte is reading people and then acting accordingly to negate their strength and exploit their weaknesses. And as we have seen from the playing ground scene, thats a skill he learned and improved/trained from an very early age. I mean you are basically trying to answer the nature vs nurture question and there probably is no easy or right for every situation answer. Was the MC genetically predisposed so that acquiring these skills came easier to him than the avg bloke ? Possibly, maybe even probably.
You are correct here, it is something that he trained. That being said, not everyone can be manipulative like that, they must be born with it. I highly doubt, that I can be in fact manipulative like the MC if I just train it. I can maybe manipulate a certain set of people, but not just anyone.
Now I don't know to which invasion you refered to earlier, but let's take an example from history, the russian invasion of Afghanistan. The afghan people were always incredibly crafty, hardy and had a huge advantage in knowledge of the land, but they still got their butt's kicked by a better trained, better equiped russian army, untill they themselves got training and equipment and they they slowly turned the tide of that war.
Just to mention the invasion that also happened to my country was a part of history. I don't really want to talk about because I do not want to talk about it. I do not want to use my country for something as petty as this argument.
Of course that better trained army will most likely win, but the word always was used which means 100% true. Better trained army is certainly more favorable, but is one of many factors that can change the tide of a war.
Leaders, tactics, technology, terrain, weather, morale, instinct to name a few are also important, not just the army.
So I guess the best I can say is, genetics can influence how fast you learn and how fast you can adapt, but wether its professional training from experts or a person training/learning by themself, I would always bet on training and expirience over genetic predispositons.
If we are talking strictly about the army (soldiers) then yes absolutely I would bet on training and experience, because it wouldn't make any sense otherwise.
But what I am trying to say that the most important people in the army are the leaders and tacticians who most likely have also fought in wars and though their intelligence can in lead an army to the best outcome. No matter how much experience you have if you are a dumbass you won't be able to use it all.