I'm confused where the assertion about the constitution is coming from. There have been at least 5 years of lower court decisions in Japan stating that lack of same sex marriage is unconstitutional. See the below article noting that the current ban on same sex marriage is due to civil law, not the constitution.
https://apnews.com/article/japan-lgbtq-samesex-marriage-ruli...
I mean, lower courts don't mean a lot in the grand scheme of things, for better or worse. It seems clear that the lower courts are trying to legislate from the bench in service of a moral good. The constitution is extremely unambiguous about this:
With "両性" unambiguously meaning "both sexes" and "夫婦" unambiguously meaning "husband and wife".