>Surely Japanese characters should not be treated the same as Mandarin ones

No. In Japanese, how you read/pronounce a character depends on context. Sometimes they are the same as Chinese, sometimes not.

Take mountain (山) for example.

Using the Chinese pronouncation it is "san". 富士山 (Mount Fuji) is ふじさん "Fuji san"

Using Japanese pronouncation it is "yama". 山登り (Mountain Climbing) is やまのぼり "yamanoboru"

(and don't call me Shirley)