[...] the policy change will take effect only from the next school year, which begins in April in Japan. The local government is still following the central govenment's directive at this moment.
Is the past perfect still correct?
I think you are right. If classes have not yet finished in Japan, the present perfect would be more accurate: students at Osaka shools are still subject to the old directive.
However, the author of the article may have decided to use the past perfect because, as I said in my previous post, the new regulation has already been adopted and reference is being made to the passing of the regulation, not to the effective date of the policy change. Legal provisions very often establish a future date for effective implementation (Starting from April 2019 students at Osaka schools will be allowed to use mobile phones). The municipal authorities had followed the national directive up to now but have already decided not to follow it any longer, and it is this decision already taken that has led the author to use the past perfect as a way of showing that the old directive has already been discarded and a new one will be in force soon. The beginning of a new term seems to be the right time to start with the new directive.