The additional footage for the extended version of the movie was mastered for the laserdisc release. From what I understand, Fox didn't want to go back and remaster the footage again for DVD, so they used the LD transfer. I haven't seen any details released on the Blu Ray but if they intend to include the extra footage for the Special Edition, they will have to do a new master.

I recall the original DVD being released fairly early on with a relatively cheap price tag, as well, so I'm not surprised that the quality isn't the best that it could be.