So here is what I suspect:
Dream Theater Historical Recordings: Portnoy took it upon himself to archive all of those so they were never in a central "DT archive" and he is not willing to give them up. Legally, I think DT could get those back but it would be drawn out and messy and not for certain they could so they probably don't even want to bother. I do think DT is legally entitled to those because when Portnoy recorded those, he may have used his own DAT recorder to plug into the soundboard, but the soundboard was still DT's, the music is still DT's, and the intellectual property is still DT's. But like I said, it would be messy and DT just doesn't care that much. Thus, we will never see any future bootleg's from pre-Mangini material.
James LaBrie as an archivist: I don't think James or the rest of the band was really into the bootlegs. I wouldn't even doubt if he has never listened to things like the making of SFAM because to him, most fans, and most musicians, they come from the old school where you buy studio albums and live albums and you pay to see them in concert. Thats it. So when he took over the archival for future releases, they probably had the idea to just release the Happy Holidays CD for free and nothing else. When I heard James had taken over the bootlegs, I thought "Awesome!" When we got the Happy Holidays bootleg I had mixed feelings. Obviously it was incredibly cool and I am so glad they did that, but I realized they would probably never go back to the bootlegs we knew. I don't think we will ever hear a ADTOE demos bootleg with the drum machine. I don't think we will hear a Making of DT12. Since they don't rotate setlists, there isn't anything live to hear that we haven't. I don't even think that kind of obsessive thinking is on JLB's radar.
So it sucks we won't get more but the whole bootlegs thing was abnormal to begin with so and that was a bonus anyway. So if there is the potential they do something again like Happy Holidays then that is above and beyond what we should expect as fans.