I suspect they did get the message since their Eparchy here in America is part of the IOCC. The Moscow Patriarchate is raising the money within its own canonical territory. Likely it is coordinated with the IOCC.
The local Autonomous Orthodox Church of Japan is our partner (working through IOCC) in providing assistance to all Japanese, of all faiths or none.
So if the local Church also has need, it is fitting to strengthen it, both in meeting the needs of its own people and in its service to the nation of Japan in general.
Moreover, the Church of Japan is the fruit of missionary efforts of the Russian Orthodox Church, so the Russian Church has a special relationship with it. St. Nicholas, Enlightener of Japan, a Russian who brought Orthodoxy to Japan, is mentioned every week in Vespers (at least in the OCA) and commemorated on February 3.
http://orthodoxwiki.org/Nicholas_of_Japan