More and more, the music industry is getting back into the mindset of an album as simply a collection of songs (if they do “albums” at all anymore). But anyone who has ever made a mixtape/CD knows that there is a “flow” to an album if it’s done right. Emotional “tension and release”. It’s like a symphony or a good film. Interrupting the intended flow of an album can greatly disrupt its emotional impact.
Bingo, JD. And I've noticed that too...the world is becoming like it was in the 50s...more single-oriented. For me, an album is exactly as you described. It's an experience that IMO, very good artists take a lot of time to work on, like QR did with The Warning before the label F'd them.
What's the exact story behind the tracklist then? Was there ever a release with the different tracklist?
Here's what happened. The band submitted the album with an approved track order (what I posted) and a mix done by James Guthrie that was more to their liking (guitars higher in mix). Once they submitted it, then went to Japan to tour. When they got home, they were told that EMI changed the track list to feature the single, "Warning," first. And they also had Val Garay remix the record so it was more in-line with the sound that was popular at the time (drums more up front, guitars dialed back, vocals way up front). The band were absolutely devastated. I recently interviewed Dave Morris, who was the band's first guitar tech and crew member. He reiterated to me how absolutely crushed and upset all five of the band members were when that happened. They couldn't fight it, it was their first record for EMI, and they had to just "move on," but it was really painful for all of them to have their work modified the way it was. They literally compartmentalized it and let it go, because they were so mad and couldn't/didn't want to revisit it.
Wait, I never said I didn't like the album in the first place. I always liked it. I just like it a bit more now with the tweaked running order. Yeah, it is cheating, but I can listen to the songs in any order I want. 
Not cheating at all. It's what the band intended us to hear. And after doing so, that album makes a lot more sense. It's an experience, as opposed to just songs on a record. Which was what Queensr˙che wanted. It's also why Guthrie was at the helm of the record (Pink Floyd). Album experiences. Just such a shame.
One of the cooler things I have is a CD that has The Warning in the originally intended order that has been re-equalized by a very capable sound engineer (not just me and you screwing with an EQ), to try and bring up the guitars, lower the drums, get some of the hiss out, etc. It sounds great. The difference is probably minor to most people, but when I A/B'd the versions, you can absolutely tell a difference.
Given what Dave Morris said to me, I highly doubt QR (or Capitol Records who I assume still own the rights to the record) will ever have that recorded probably sequenced and mixed back to something like they intended. All the band guys still have their original net final mix cassettes that they approved before heading to Japan. So the mix exists. But given that those are on cassette tapes, I hope they all digitized them. If they were to ever have the album remixed, they'd have to start from scratch, and use those tapes as a guide. And at this point, I don't see them ever bothering.
Those of you who are just comfortable with the original order, try the intended track order, and then read along with the lyrics. It's a conceptual album, and the track order makes a big difference in realizing that concept.