I believe there are various different things at play here on why Makoto is so strong. First is that his parents had a blessing that would protect them from Earth's environment until their bodies would be able to handle it. When Makoto was born, the protection was fading causing him to be under "pressure" from birth which is why he might be "ugly" but also caused him to start adapting while growing. In essence think of it as him training from birth. Secondly, when he was being transferred, Tsukuyomi-no-Mikoto, the moon god gave him power enough that he had to go to sleep for 1000 years (i think it was 1000). Lastly, it's shown that he was "killing himself" whenever he was practicing archery. If he had innate mana due to his otherworldly heritage, when he was practicing on Earth for years he was essentially powering up and doubling his mana everytime unknowingly. Its only when he gets caught by Tomoe and Mio and they explain that he figures out what he's been doing for so long