If Rakuten is charging more on their foreign language travel sites (they have Chinese and Korean too), I imagine it's probably to pay for the cost of translating everything, which makes it more akin to the expensive process of renting an apartment through an expat housing company. Complaining about this is like complaining about insurance companies that require you to speak Japanese (although some foreigners do, incredibly, complain about that too).

HIS's policy was less excusable -- charging more to people with foreign passports even if they were booking travel over the counter in Japanese just like a native. One can learn a language (or use their own translator) but it isn't as easy to learn a nationality.