Using this logic, 18th century North American Apaches have an advantage over Roman legions and Sengoku samurai armies as well!
While my knowledge of North American indians is weak I do know that in comparisons the New World natives didn't advance the same way as the Old world (I would include Japan as Old world as well).

That and one of the main reasons the 18th century Musket armies were able to conquer the new world was through diseases so I would say 18th Century Apaches would give any Japanese/Roman army a good beating as they do not fight open warfare but hit and run which the Romans always had difficulty fighting against.

That and no one seems to answer my question whether a Japanese army would actually comprise mainly of samurai.