Well even the link you provided listed changes to the DVD version, as well as further changes to the 2011 BD/3D version.

And yes, unfortunately the subtitles will not be absolutely perfect. Their vertical placement is consistent in all but one scene (a close-up of Sebulba saying "you slave scum", and their horizontal placement is consistently centred. Since the DVD/HDTV version is not cropped exactly the same, the subtitles are not in the exact position they would have been in originally. I will be making sure they are as close to right as they can be when averaged across the 27 of them (and the Sebulba one will be lower as is theatrically correct).