There is a lack and mismatch on the hierarchy of the Empire and that is also how it was on real world as well.
The Emperor has as landed vassals the daimyō of the Otomo, Miya and Seppun Imperial Families, the Great Clan Champions and the Minor Clan Champions and the Emerald Champion. They all have different values of status based on their power, prestige and familiarity with the Emperor.
The Imperial Families and Minor Clans are small enough that they don't have more than one Castle/Palace and might have a few Samurai assigned as Mayors or Governors if they have an important city on their domain, but possibly no more landed samurai than the head of the family.
The Great Clan Champions have the head of their respective families and one or other general assigned to a fortress and the respective village and surrounding land and any Clan Magistrate assigned to a castle or town.
The head of the Families have lesser daimyō assigned to the many provinces that make the land given to the family.
These lesser daimyō might have, depending on the size of the province some landed samurai that oversse a village or a town.
These lesser daimyō might or might be from a vassal family of a great famliy or might be a representative of said great family, same for the landed samurai.
Edited by Diogo Salazar