While the Priority Club T&Cs state that no points will be given for reservations made through "third party web sites," one sometimes does receive points as you have found. Nice!

Concerning Rakuten (which I use a couple of times a year usually for some in-country weekend getaways), not only does the Japanese language side have more hotel listings as has been pointed out, but often will have better prices, including, I've found, for the same properties listed on the English language side.