I'm pretty aware of DT history, though I've never read their official biography Lifting Shadows. Just going by what I recall reading throughout this site and others over the years.
About Outcry, I don't think inserting a through composed section into a basically simple metal song makes it progressive. I don't think Endless Sacrifice is prog either. Metropolis pt 1 did it first and at least Metropolis pt 1 has a more complex song structure that also has a crazy instrumental section that flows well in and out of the song proper, and feels like it belongs to the same piece of music.
Then I'd like to know your definition of 'prog', because both songs are arguably progressive metal. No, they're not 'progressive' in the literal sense that they're actually pushing boundaries and doing something new, but they contain traits and characteristics of progressive metal music. Also 'Metropolis did it first' is demonstrably false, because prog music had existed way before Metropolis was ever written, so by that account Metropolis is not prog either.
At least lyrically I can explain the middle section in Outcry and this song does a far better job at story-telling than Metropolis OR Endless Sacrifice (or a lot of other DT songs, to be honest actually..) So, regarding Outcry (again), I think you're completely missing the point to this song, because as far as I see it, it is NOT a 'simple metal song'. Let's break it down...
We start with an intro, outlining the main chorus melody in the keys, but it's unfinished.
In come the other instrument, the entire chorus is played in Bm, without vocals.
Some sort of main riff comes afterwards.
We have the verse on syncopated low B's
Second half of the verse ("the rebel in us all...") over odd time signatures
The 'Pre-Chorus' the suddenly gets quiet, as a means to build up to the chorus
Aaand here it is. But what? It's in a different key! The chorus is played in E instead of in B as heard before.
Here's that 'main riff' thing after the chorus, although played slightly different. And this time, the vocals go over this one, instead on the syncopated Bs. While harmonically similar, this riff drive the vocals more forward.
"The streets are bathed in blood" section (similar to 'the rebel in us all').
And maybe now's a good time to actually take a loot at the lyrics and what they imply. They're about the various uprisings in the middle east, and some Middle Eastern influence is actually clearly audible in the instrumental section. If you consider the last lyrical section, which I'll copy below for your convenience, I think it's pretty damn clear that the entire instrumental is actually a musical depiction of a struggle, a rebellion, or uprising. The jagged rhythms, the seemingly incoherent parts, it's almost as of the musician's are in a battle with each other as well. To me, this instrumental section makes so much more sense than some of the other instrumental parts in DT's songs that really seem to be put in just to be there. This one actually has a purpose,
"The streets are bathed in blood
Time to step down and time to walk away
You'll never rule me now
Though you may stand upon my grave"
---
After the battle is over, we get to a piano break, the 'aftermath' so to say, followed by the "Freedom's worth the fight" lyrical section that's almost bleak in nature. James's vocal delivery here portrays the hopelessness of the situation, but then we get to what's arguably the best part of the song, which is the last time the chorus comes in.
This is
not a triumphant return to the the chorus, one that's even more exaggerated by the fact that it's repeated twice. Having heard the chorus just once so far (in Em) at the beginning, it may have felt glorious back then, empowering, with high vocals to back that up. This version at the end is a fourth lower, in Bm. I'm absolutely sure that this is an intentional song-writing choice. Playing this chorus lower than the original emphasises that the entire situation is hopeless, though the rebellion is till trying. The last lines of lyrics further drive this point home. "Locked in a kingdom of fear, as our children die."
---
Quick recap, without even dissecting the instrumental section:
Intro
Intro Pt. 2 (Chorus Riff)
Intro Pt. 3 (Main Riff)
Verse 1
Verse 1 Pt. 2
Pre-Chorus
Chorus
Verse 2 (over 'Main Riff')
Verse 2 Pt. 2
Instrumental Section
Break
Different Pre-Chorus
Chorus in Bm (twice)
Outro
That hardly looks like the structure of a 'simple metal song', unless you'll twist that definition.
---
I know I said in a post above that Outcry might be the 'most progressive' song Dream Theater have written since MP left the band and while I of course can't be certain of that, I think it's worth noticing that this song is actually about some meaningful, a real-life event and it tries to depict that musically as well as lyrically. A lot of the so-called 'prog music' (DT often included) often doesn't do this and plays stuff for the sake of playing, with lyrics tacked on to the track that don't really mean anything, or seem like an afterthought. I know that's generalising, but I hope you get the point. Outcry though, is a synthesis of both the music and lyrics and the more I think about this, this song is far better than people give it credit for.