I've made a couple of tweaks to the version summary above to appease my OCD tendencies!
Bottom line? Even if the 4.1 were based on the 6-track mix, it's apparently been tampered with (possibly at the director's behest). This leaves the 1999 DVD and the 1995 laser as the best sources for the original mixes.
Our Mission Should We Choose To Accept It? Create a theatrical preservation using Blu-ray video and the two audio tracks from the earlier DVD and laser releases. We could go further and look at colour correcting the video too (since it's undeniably altered from the original release), but that rather depends on how much it bothers people - I personally don't mind it, but I know it's an issue for some. We might also include the 1999 commentary and production audio tracks, seeing as these didn't survive the transition to Quadrilogy nor Anthology releases.
I can probably do most of the actual assembly and authoring, but the one thing I don't have is that laserdisc mix. Let me know what progress you make there!