... also strange that they don't make bitcoin legal when they are accepting it as a payment, sound weird to me...
I think that Japan is also playing safe in this case. Yes they will accept bitcoin as payment, however legalizing the bitcoin itself as a currency used in Japan may be a risk due to bitcoin's instability. Not legalizing the usage of bitcoin immediately but accepting it as payment is a wise move, in my opinion, for Japan so that they can easily ban bitcoin if they encounter any critical risks.