I've never seen the LD, but it was always analog audio only even on the restored Encore editions. I'd say since you've got it it should be compared to the 99 to see the differences. It might even be good enough to be made into a lossless soundtrack.

The 06 audio is bad but in slightly different ways than the 04 audio was. It's processed slightly but highly degraded.

I haven't seen the HD version (still need to) so I can't really tell if it's the 06 or not. Judging form the caps I think it is and so I would believe it has the same audio.