You're making a mistake by confusing "wealth" and "ownership of the means of production". Under feudalism, the means of production are land rights. Merchants don't have those; warrior-nobles do. The ruling class is the class that controls the means of production.

I will say that a feudal society where you have merchants/factors/etc becoming richer than the feudal nobles is a society in transition. The Japanese example is no different from Renaissance and early modern Europe when capitalism was in its earliest stages.