It's a good question, here is my geeky blathering take:
Think something like Enya, how those atmospehres sound so lush
It's about how it's mixed and obviously recorded.
Instrumentation: Reverb (on vox as well), ethereal guitars, strings, synths ....whatever.. Like how the end of Streets sounds like it's in a tunnel and the chiming notes seem almost endless until they drop out. You can hear the end of OOTS very similarly but it's very direct and loud, it does sound good but certainly less atmospheric. Maybe it has less reverb, but being so loud does take some of that 'space' feeling away.
When Edge plays the delay effects, those are repeated notes, if he plays over them you don't hear them echoing. Again, it may have less reverb as well. Very possibly less delay as well. In fact I am pretty convinced of that, probably should save that for the guitar forum.
Most importantly it's allowing the listener to hear all of those atmospehrics.
When you go for more volume sometimes you lose the quality of the atmospherics. think of the harmonies on the Lemon "man makes a picture" which I think is just Eno and Edge, sounds very atmospheric if not hauting, and also quiet. Or the harmonies on Walk On (album) same effect. If you push that louder you can lose not only some of those vocal qualities, you hear the main voice less, the guitar less etc.
HTDAAB, because of the industry in general wanting more loud music for more amplified stereos etc, and the fact that it's supposed to be a more direc effort, I think you get more of a 'loud' feeling as opposed to an atmospheric feeling. You can barely hear the strings in Sometimes You Can't Make It On YOur Own, because they are so far in the back, that was a great atmospheric that was there but wasn't audible enough IMO.
Also Bono has been singing w/o much vocal processing if any at all. Like most of everything from UF-Pop he sang quite a bit thru processors (think the low parts of The Fly) or even Gone, reverbs and maybe even slight distortion. Bono, as it sounds to me, is singing pretty much with his naked voice on HTDAAB (ATYCLB as well, possibly) so it has to be louder. So if you make him louder, you gotta compensate throughout, the whole thing becomes louder.
I think a lot of it is really just mixing.
take 'Heartland' it has that very lush moody atmospheric.
I think part of it is Bono's baritone, the mixing and even how the bass sounds, where the higher end is less dominant and you have that really deep pulsing bass, like Please for example. The bass on Vertigo, for example is reverbed, sounds more 'punk' less moody and on ABOY it sounds like 60's rock. SO it's also intentional aside from production techniques.
Basically they were going for a less atmospheric sound because a lot of those atmospherics compensated for lack of musicianship in some ways. These days they are a more confident band, from voice to bass to guitar and drums in terms of how they sound 'raw' but in an effort to sound more direct, less moody, maybe even less pretentious, they sort of sacrificed a lot of that.
What I mean is a song like 'Electric Co' has all that delay and it just echoes and really creates a swirl in your head, where on COBL or Miracle Drug he's using less delay, less repeated notes and actually playing more because he doesn't want to step over himself.
I don't know, something like that.
the term is definitely overused, but the "otherness" is the perfect way to describe it. It's a feeling, for me. I can't say "this song is atmospheric because it has this sound in it," it's the combination of sounds that somehow make a piece atmospheric. Sort of other-worldly, almost. Music you can get lost in. 
