Slightly disappointing reprint of a masterpiece
Having now listened to both prints I'd like to state that there are indeed a handful of tracks that suffered from the 2006 remastering. Sometimes echoes are lacking or are too pronounced, and some sounds now come with a slight "crack".
So yes, inferior version. But chances are most people won't notice unless they are very familiar with the original material.
All in all nothing that should drive you away. As this is still one of Sakimoto's very best (and my personal favorite).