Wow!!

Sadly that's all I have to say. Even if I knew more Japanese I feel like this would be hard to make out.

I found out what this is about!
This song did not originally have a second verse. However, shortly after Utena, there was an... event... that was a collaboration between Seazer and Ikuhara, a one time thing that did not get a CD, called Jyuutaism, somewhat connected to Utena but I'm not sure to what degree, and the lyrics to that are at http://www.geocities.co.jp/Hollywood-Ko … mkasi.html. This is the source of the second verse to Absolute Destiny Apocalypse. I found a couple of different sources in Japanese (which I can link to if someone wants) saying that this verse, unlike the first verse, actually was written with Utena in mind.

The lyrics sung on the CD that includes this song... sound very different from how they're written on this page, in several places... but the first verse also isn't sung as it's written, so that's not much of a surprise.
Here is my first translation--based only on how the lyrics are written. Later, I would like to attempt to figure out what they are singing when it's different and how that would affect the meaning, but this is what I've done already. The written lyrics are actually mostly straightforward; the only line I'm not sure about is the "I am breaking twenty-one" one.
Absolute destiny apocalypse
Absolute destiny apocalypse

Oriental origin, Orpheus, androgynous mystery record

Absolute destiny apocalypse
Absolute destiny apocalypse

I, Protogonos, lip-egg, apocalypse

The seven me’s from the iron egg,
The seven mysteries from the world egg

I am breaking twenty-one
My I, my Prakriti

Illusions accompanying absence
__ binding egg child,
Astronomy advance notice fusion
Both sexes eternity principle

Heaven and earth, day and night, sun and moon
Men and women, androgynous: apocalypse

Mokushi kushimo
Shimoku kumoshi
Moshiku shikumo
Mokushi kushimo
Shimoku kumoshi
Moshiku shikumo

This seems to have been heavily inspired by Orphic cosmology and  their creation myth, which I don't know about. That even explains the "oriental origin" line, as the Wikipedia page on Phanes/Protogonos says, "Scholars have suggested that Orphism is 'un-Greek' even 'Asiatic' in conception, because of its inherent dualism."
The __ is because the page has asterisks instead of the kanji for that word... some of the other songs have more of those. I guess the person making the page was working from an incomplete source...

That is all fascinating! I posted the translation very soon after making it, so I'd only done cursory research, but I looked into it more today and I think you're right. Actually, I'm quite struck by how closely it resembles Gnosticism, which I have extensively researched because of Utena.
I'm struck by how Wikipedia says Protogonos is also known as Erikapaeus, meaning power, and Metis--which links to an article about a goddess. Protogonos is said to be both male and female and Anthy's closest counterpart in Gnosticism is Sophia, the wisdom principle--Metis means thought and is a goddess of wisdom and cunning.
Basically I think Protogonos might represent Dios, Akio, and Anthy, the way Abraxas was believed to be both Christ and the devil.
It's also worth noting that Orphism uses the symbol of the World Egg quite extensively. It's not the source of the "The egg is the world" quote, but it's relevant to it.

"This Herakles [referrin to Chronos, not... Hercules. the names are confusin) generated a huge egg, which, being filled full, by the force of its engenderer was broken in two from friction. Its crown became Ouranos (Uranus, Heaven), and what had sunk downwards, Gaia (Gaea, Earth). There also came forth an incorporeal god [Protogonos-Phanes]."
Sophia in the Gnostic tradition was also thought to have sunk into matter as a result of her fall from grace.