I find it unlikely, but has anyone found a bootleg recording of the concert in Japan? The Final Boss Medley had FF VI final boss theme besides One Winged Angel, and perhaps all the other pieces in the medley were arranged differently. Thanks in advance!

The two FF VI tracks are "Mystic Forest" and "Kefka", and the new medley was arranged by Roger Wanamo.

I think you mean this one

Symphonic Fantasies 06 - Encore (Final Boss Suite) + Download Links - YouTube (http://www.youtube.com/watch?v=7XeZ0gjB414)

But there's no FFVI final boss in it.

No, that's the original Encore from the 2009 performances in Germany. The concerts in Japan happenend on the 7th and 8th of January, 2012. According to impressions and reviews, the Encore there was a different one.