First of all, you're not supposed to post a published map without the permission of the publisher, in this case AE. So I'd delete the map image from your first post if I were you.
Secondly, geologically speaking Rokugan isn't necessarily an unrealistic map. I think the argument against Rokugan, is that its supposed to represent fantasy Japan - and Japan is an island nation. Rokugan, geographically resembles China and not Japan at all.
I happen to publish (as an imprint under Rite Publishing), the Kaidan setting of Japanese horror (PFRPG) - I also happen to be somewhat of an ancient Japan expert, especially regarding folklore. Kaidan, like Japan is an island nation. And really lots of detail content of the setting was intended to correct mistakes made by both Oriental Adventures (D&D Asia) and Rokugan regarding culture, technology, history, folklore and more. The point is what make Japan different from any other Asian nation is entirely dependant on the fact that it was an island nation, unfettered by invasions and most other outside influence since it doesn't sit adjacent to some other country. Being an island both protected it culturally and kept it isolated from the rest of the world to develop the uniqueness of that which is Japanese. (I am half Japanese by the way.)