It is possible to run maintenance at different times for Japan and NA and EU. The NA/EU is in one data center and the Japan servers are in another, so it is very easy for them to schedule 2 different times.

Furthermore, if they partition their servers so EU and NA are not sharing resources, they can also create 2 separate patch times for them.

It is very easy for them to avoid screwing over one playerbase or another. Big game companies just don't care. They don't want to spend the time planning 3 different deploy times and really couldn't care less whether you are online or not during that time of the week. If the game subscription was paid for hourly, it would be a different story. They would be looking at ways to patch without taking down the servers at all.

It isn't though. It is paid for monthly.