The tapes of the original albums were provided by Abbey Road, where they were transferred to high res masters. They were then given to Universal. They decided in the end to boost the levels of the early albums for the CDs as they were so much lower than anything else released in the last twenty years. Don Bartley then ran it all through his gear to give it more body. Neil might have been involved with that too - I'm not sure.
The vinyl was mastered from the same hi res masters but without the processing done for the CDs. Not sure if Intriguer and Time On Earth are new cuts or the same as the originals.
My guess is that "I Walk Away" was faded early during the mastering of the album in 1986 and this was repeated for the DVD-A stereo master and 5.1 mix.
"Together Alone" is the same mix, as far as I can tell, so I suspect the cheering was cut off during the mastering of the original album and reverb added.
The new vinyl of both will have the extended versions. I don't if Universal intended - or knew - about the differences, but I'm glad most people approve so far.