Em............some of that goes into more techie stuff than my knowledge covers but according to this:
http://en.m.wikipedia.org/wiki/The_Abyss#section_5
Then Cameron (per the history of the SE section) was the one who spearheaded the work to redo 'The Abyss' and it did get a limited theatrical re-release in 1993. But that's because I think Cameron would never let a version of one of his films go out without being involved in whatever version it was.
I don't think 'Aliens' had a theatrical re-release. But wouldn't they have needed a film version for the work to transfer to Blu Ray for the Anthology? Or am I quite wrong?
When it comes to TMP I don't know if it was ever asked why the new effects were only done in SD and not HD. I guess perhaps there may have been a sense of 'it's only for home viewing though'. That's possible. Does that mean the Blu Ray edition available is the 1979 unaltered version? I'm still using the twenty disc 2002 Special Collector's Edition DVD box set for the original films as I'm not satisfied with the options and/or packaging of the ten films on Blu Ray so far.