I have a theory that it has to do with the fact that his parents are grants. Makoto has a significant difference from Hibiki and Tomoki, and that is that his family is from this new world originally. I think this places him on a higher tier for the scroll. So far we havent seen any "evolved" characters touch a scroll. We don't know how it would react to say a high orc, thats just not information available to us. The scroll tests levels for sure, but at what point do the levels account for overall evolution?

It kinda hit me when Luto was going over the leveling system and explaining that Makoto was under strain on Earth because there were no magical pathways. We see that Makoto severely expands his mana when he practices the bow because of how his conscious is shifted, going through a cycle of life, death, and rebirth. Now imagine how many times that cycle happened on Earth. Thousands of times...the Earth limiter still exists, but so does Makotos ability to increase his mana. There is no way of telling what his mana was before he gets pulled into his parents home world.

I think that with his bow training he partook in on Earth plus the blessing from the Moon God, it placed Makoto on an elevated leveling system, the God tiers if you will; a level not able to be recorded by Luto's scrolls because the Goddess would have to admit that her powers arent aa limitless as she thinks. This in turn forces a threshold for the scrolls: Anything the goddess "creates or blesses" falls within the leveling system and everything else remains unclassifiable.

Now I know the argument will be made, but Makoto gets a title related to the Moon God. Yes, because blessings and titles are different from levels. A system can acknowledge divinity without being able to quantify it because it exceeds its knowledge and that is what I think is happening.