As for the different fades and full endings etc... Who would have a problem with that unless it is a shorter version/edit than the original. Hearing the full end of "Can't Carry On" was a pleasent surprise although I first heard it on the 5.1 mix. (The surround mix was so different to the stereo with variations a-plenty!).
I'd have a problem with it, in principle (this is all subject to be understanding of the term remastering being completely wrong!). Remastering bringing out detail you've not heard before is one thing, but changing the song in more fundamental ways is completely different. Your assumption seems to be that making the song longer is OK, but shorter is not OK. If I bought a Pet Sounds or Revolver re-issue, I wouldn't expect (or want) God Only Knows to have an extended intro, or I'm Only Sleeping to have an extra chorus. Those become alternative versions, in my eyes. Any argument that it's 'in the spirit' of the re-issues isn't really correct either, in my opinion - the albums should be as they were, alternative versions should be on disc 2.