Wonderful! Simply Wonderful!
Supporting your broad argument, in explaining the alliance of Yanagita & Minakata with regard to the Shrine Consolidation Program, in his 2005 Master's Thesis, which is devoted to a parallel but distinct topic -- the early roots and subsequent development of Japan's New Left -- Manuel Yang writes:
It is true that, although Yanagita and Kumagusu opposed state Shinto they both respected the tenno. (Yanagita had worked as an imperial secretary and participated in formal ceremonies of the imperial household while Minakata had given a lecture on his research in botany and bacteriology to the Emperor in 1929). But their tenno was not the tenno to which the bureaucratic modernizers had appealed to legitimize their policy of state-building and capital accumulation, both of which assaulted the commons and expropriated the peasants.
Yanagita, of course, is the scholar most responsible for the academic view of Japan as a unique culture ordered by the the collective necessities and rhythms of rice cultivation. He and Minakata eventually split over Minakata's insistence that a) Yanagita's theory was both empirically incorrect and b) Yanagita was allowing himself to be be used to provide a historical and anthropological justifcation for increased authoritarianism, centralization, destruction of natural resources,
Though there is no firm evidence of any substantive contact between Ueshiba and Minakata in the years after Ueshiba's departure to Hokkaido, It is a curious coincidence that Ueshiba's retirement to Iwama falls closely after Minakata's passing in 1941.
It would seem that, as with the individuals of the time, so with the factions -- whether their interests were capital formation, commons retention, nativist religious fervor, agricultural arcadianism, enviornmental preservation, or some heady mix of these and other elements, all contended for the newly raised banner of the tenno in the language of the cult of the emperor.
It was the only game in town, and that goes a long way to explain the motley aspect of the crowd at the table.
Many thanks for the many connections you have drawn.