It's just a supposition, but I would make the guess that the SEED are another form of the Darkness ~ manifesting in a somewhat similar manner to the GERM from PSO EP III. Photons and A-Photons (A-Photons are processed from Photons) are likely the remnants of the Great/Holy Light. Hence, the reason why SEED are attracted to A-Photons. It's a continuation of the battle which started millions of years ago.
I would guess that there's a greater evil, much like the Profound Darkness, sealed away within the Gurhal system... which is controlling the SEED. This seems somewhat plausible at least, since the very first appearance of the SEED had them emanating from something that looked like a Sun embroiled in sunspots. Weither it's Gurhal's sun or not, I don't know - but in the chapters leading up to the Unification Point, there's mention of increased sunspot activity in Gurhal's Sun.
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