Trying to gather my thoughts for the Light Wing entry, but they’re all tied up in this larger scenario right now anyway, and even though I really should be getting some sleep… 
Since the guide translations have somewhat restored my own default settings about a number of issues, I’ve been thinking in terms of revisiting all the basics as though fresh. And it doesn’t get more basic than Panzer Dragoon (Eins):
The story of the original game - such as we were given one - seemed intelligible enough on it’s own terms. A militaristic empire is excavating a mysterious and presumably exceptionally powerful ruin, seeking even greater knowledge and power for itself. There is a battle in progress between two warriors, both riding a dragon - fearsome specialized weapons of the Ancient Age. One of them is evidently trying to reach the “Tower” ruins, the other wants to stop that from happening.
Why? At the time I remember thinking the Dark Dragon and it’s rider were obviously members in that evil empire, trying to rendezvous after some big discovery or milestone or something. While the Blue Dragon and it’s rider were clearly from some opposing nation, trying to stop an event that might give their enemy an insurmountable advantage.
Well, it did seem fairly obvious to me at the time… but it also didn’t much matter. Being in that world (and shooting at everything in it) was just fun, so who cares about the details when they’re so thin anyway?
Of course all those impressions are radically recast once I’m playing Azel, and I assume nearly everyone had a similar experience if they had been with the series from the start. But consider again those elements as they stand on their own: that Sky Rider who implores you (Kyle) not to let “him” go back to the Tower… well ‘he’ evidently already knows and fears something very definite about those ruins - and what will happen if the Dark Duo reach them.
We were given a depiction of two well matched elite warriors, engaged alone in some turning point conflict. One falls, and the humble outlander must pick up his cause, and join his battle steed before all is lost. It was brilliant of course. But was it actually even as misleading as may seem from subsequent revelations? If one even agrees with that impression - what if there was no anticipation or intention to mislead? And if the authors also remained true to the substance underlying that impression?
Was this indeed two seasoned elite warriors, who know one another quite well, at least by record and purpose. Perhaps even met in battle before… yet ages ago. One way or another, that Armored Blue Dragon’s rider seemed clear about it’s objective, and the stakes involved, in a way no other “mediator” could be, at least until Edge himself learned enough from a dozen different sources.
Letting that sit…
My first impressions about the Solo Wing Dragon transformation, were that it was more of a stylistic ‘updating’ of the classic Blue Dragon. I didn’t think much beyond that until playing Orta, and was initially almost disappointed to see the ‘stubby’ older looking design (I got over that quick, they’re both great) and the label “Blue Dragon”. So that first cemented them as distinct entities in my mind, even then, it was really only after I started thinking of the Solo Wing as more than an Easter egg, that such distinction seriously meant anything. For the sorts of reasons I’ve already stated: once the Solo Wing transformation is considered consequential, then there is also a great mass of consequence leading up to it, that had been almost entirely passed over. Including much about the Light Wing.
Again letting that sit, too many details heading too many possible directions from there, away from the motive of this post. A lot in my old Zoah theory topic, but too many of those details seem to dead end as well. So this is mainly just to frame my larger motivations about this almost ruthless theory outline that kept me from getting enough sleep tonight…
Let’s entertain the notion, as abstractly as possible, that there is no ultimate or “complete” canonical table of events. What if the purpose of the Type 01 transformation at the end of Zwei is not to establish any fact of how the Eins dragon arrived at it’s form, but more to affirm continuity as something that hypothetically could have happened. You had recently asked about the Epilogue A crest Solo, well it’s also chosen for the end-of-the-line image of the Zwei lineage in that wallpaper (and is it also the cover of the Japanese version?)
By the same token, the Light and Solo Wings may both be considered bonus scenarios. They require a lot of extra - and entirely non-essential - travel all right as you’re ready to finish the fight. And the Red Ruins are an entire set piece area built around ritually cannibalizing a dragon pup you’ve dragged half way across the map… and nothing else! 
In a sense it’s equivalent to all the other books and texts you may (or may not) find, embellishments to the back story, but as experiential packages of data.
So the basic outline I’m mentally/emotionally testing right now, goes something like this:
Some loose incarnation of the Heresy dragon indeed existed during the fall of the ancient age. Battles were fought, won and lost.
Various agents of bio-technology were put on ice all over, certainly including Azel, Atolm and Abadd, so why not other dragons and drones from any and all other factions?
But the ‘Will’ of the Heresy dragon, the Will of it’s true creators, is something both more powerful and profound, yet perhaps more vulnerable and not so easily hidden away, than any mere biological system.
Once that Will is forced to act, perhaps prematurely, it must protect itself and attempt to further it’s objectives by any means possible. Once the Heresy program is identified and purged, Sestren has essentially immunized itself against further contamination by that pattern, so direct channels of influence over other systems wired to Sestren in any way are for the moment blocked.
The best it can do, is a most inauspicious genetic host in one of Sestren’s few blind spots. but of course, it will still do. Long enough and well enough to get back on the offensive, and even find/make some conditional gateways back into the system. If in rather blunt fashion.
The event itself was brought to a close when the dragon destroyed Shelcoof, and petrified part of itself within the Tower in order to thoroughly seal away its functions.
And… why is it such a priority to seal away Shelcoof’s functions?
The GD was a dragon left behind during the reign of the ancient civilization by the Preservation Faction in order to guard Sestren and the Towers. In addition, it was imbued with the will to eliminate the dragon left by the ancient civilization?s Destruction Faction upon its appearance.
Again, it can be inferred that these two may have tangled before, in some sense or another. If the Heresy program embodies the primary will of opposition to Sestren and the Towers, then it would seem this Guardian and it’s charge are one of the prime embodiments of the will to counter it.
It might have taken nearly everything this incarnation of the Heresy program had left to both seal Shelcoof and still project enough of itself towards other endeavors. And one of those endeavors could well have been reclaiming a purpose built form, in preparation for the threats and missions it knew would come.
Why are there two pedestals in the Red Ruins for Dragon Crests, and more importantly, where did the one that was missing go?
And exactly what purpose the Sky Rider was intended to serve, if ‘he’ was a drone, is unknowable. But if things were actually so strict, as such, about the “mediator’s” required lack of bias, then the Divine Visitor’s role becomes more of a paradox. Since the dragon’s self avowed purpose was to lead it to actualizing that agenda all along. I think the final decision needed to be placed in the hands of a human, but not that of every single act of opposition and aggression. Lundi describes the feeling of being compelled by the dragon’s objective, even though he knew nothing about it.
OK, to be continued in some fashion…