Not really! As my last experience on Osaka Marathon, we still registered by sending the email directly to the registration on Early Aug almost half-year after the deadline. So please try sending the email to registration if you don't want to go thru Travel Agent. The travel agent told me that they were the only channel for late registration when I asked them for the Osaka Marathon registration case. Anyway, my Osaka experience is so wonderful. I believe Kyoto shall be great too. Enjoy!