I think the new master for Episode 1 may actually have been done mainly for the 3D conversion, as they would need to have a complete digital copy for that and the old DVD master wouldn't be good enough for theatrical presentation.

Although, what I find curious is that it is documented that there were digital projections of TPM in 99, so why didn't they use the digital copy made for those projections for the DVD? I doubt that it could have been the same master, as the current DVD transfer (and its HDTV 1080p counterpart) wouldn't withstand the test of a theatrical presentation very well at all.