I am disappointed to see this, but I think I understand it.
Most likely, the porting of the Japanese version of each platform to the NA version of each platform is a separate process for each platform. The cost of doing that port for the Playstation 2 plus the cost and other factors involved with distribution of that disc after it's been made to North American Players is just too high for the quantity of players that will actually want to use it.
There are a LOT more Japanese players still playing the PS2 version than there are NA players on the PS2 version. Japanese players like playing on consoles. NA players tend to play on PC much more. That's not to say there are no PS2 players in North America. They do exist. But SE now believes the quantity of them is now low enough to not be worth the cost of porting and distribution of a new title for Playstation 2. (And Sony may not want them to either.)
I see it as a business decision. If it costs more to make and distribute that disc than the amount of revenue they can earn from those players, it's best to just let it go. They also do know that many of those players will get either a PC or Xbox 360 version somewhere along the line, so they won't lose all of them as customers. They will likely lose a few. SE doesn't think it's enough to be a problem.
I do believe it has nothing to do with "PS2 Limitations" or trying to get rid of them.