The timeline fits: "Sakamaki Deido [aka Makoto] was the first child born into a textiles family in 1904." I'm guessing that after he went back in time through the timestream, he was taken in by a family. Without Grandpa there to imbue him with super nano magic, he started aging normally. "Around the time of the great earthquake of 1923, his mannerisms began to tend toward the peculiar. At the time, he was traveling the world, [...] but when he returned in 1925, he pawned off his belongings and began building Souboutei." The great earthquake of 1923 might've been the first stirrings of the Moray that went into the time stream with him, which had been quietly recovering underground, and which Makoto might've assumed dead. He then built Souboutei in order to supervise the Moray and prepare for his brother's return. Perhaps, he lost his shapeshifting powers as he aged: after all, his cells would've been replaced by new ones that hadn't been touched by Grandpa, and that's why he couldn't kill the Moray after becoming aware of it.
Now, the question is this: why does Makoto appear young once again? Did he strike a deal with the Moray in order to extent his life until his brother got there? Was he possessed, but somehow remains in control and uses his art to keep his composure, in order to fight the slugs inside him ("My artistic expression is nothing more than a medical examination")? Has he been partially possessed since 1938 (three years after Souboutei was finished), when the first painting was sent to a Prime Minister, and after which there's a 35 year long gap in the records? Did the Moray possessing him reverse his age in order to keep him alive longer? If Makoto is connected (through possession) to the main Moray that has merged with the house, is that why he can exert some small power over the black water and aid Takoha with the black arms?
Also, the year the airplane was apported (connection to Flor, somehow?) into space was 1972, the same year the PM, DM and their friend went into Souboutei. The plane thing happened at New Year's, so it happened shortly after the girl was... cloned?