Yep, it had the seven eyed mask since the very beginning :
Since the explanation of Evangelion states that it was excavated from the Moon, that the bump in the torso imply that it had a core and that Lilith have a different mask in NTE, the most likely explanation is that it's one of the four ADAMs, like EVA-13 many years later.
And indeed there was an unused storyboard(or script I don't remember exactly) for the 2I flash-back were it was shown that a giant spurt of blood erupted from the vortex and left the big blood streak on the Moon and implicitly ejected one of the ADAMs and the LoC with it.
wiser3754 wrote:The lingering questions about Mark.06 are as follows:
-It merged with Lilith, but the FOI are in EVA-01's image and Lilith bares no resemblance to Mark.06, why?
-It held the Cassius (now morphed to Longinus as Kaworu concludes) spear in an attempt to impale itself or trying to stop it's attacker from impaling it, which one is it?
-The twelve angel was found alive inside of it, whether the twelve angel was powering the Mark.06 at first (hence Mark.06's halo in 2.0 and briefly shown it 3.0) , the twelve angel made contact with Lilith and set off 3rd impact (FOi and Lilith's image don't add up with the exception of the head) or the twelve angel (made entirely out of core, wink) was born of Lilith via the merger of Mark.06 and Lilith.
-Made into an autonomous type, exploited by NERV and SEELE and brought to ruin. Why make it autonomous and what made it autonomous, dummy plug or the twelve angel taking control of it?
Any more lingering questions that I've missed, or these have already been answered, comment.
- Since Lilith's corpse is atop the pile of skulls(which most likely belonged to the FoIs) the more probable explanation is that the FoIs were created before Mark.06's intervention. As for why they are at EVA-01's image, again it's a mystery, a possibility is that if like in NGE Rei has Lilith's soul and 01 was directly made from Lilith's flesh, then when Rei was absorbed inside the Eva and it awakened, it created a "mental link" with the rest of Lilith's body, and when said body activated it created the FoIs at the image of the current body her soul resided(EVA-01), that would also explain why Lilith got Rei's face too.
- Looking at the position of Mark.06's arms, outstretched, it's clear that it was impaling itself. If he wanted to pull out the spears, the hands would be closer to the penetration point of the lance.
- Since it's implied that Mark.06 is one of the ADAMs, that must more likely be the reason why it could fly and had an halo(remember that Mark.09 could do the same thing, and EVA-01 got an halo during a brief time, and none of the two had an Angel inside them, most likely they are Angels themselves). As for what the hell the 12th Angel was doing inside Mark.06, we don't have any idea. If it's the Rbuild equivalent of Armisael, then maybe it tried to possess Mark.06 when they were fighting and then fuse with Lilith, or it attained Lilith and started 3I and Mark.06 descended to stop it, and then tried to fuse Mark.06 with him already fused with Lilith(explaining why Mark.06 was fused with Lilith's neck stump and inflated to the insane size it ahd when EVA-13 met it 14 years later)
Maybe it's something else, we don't know.
- we don't have any single idea either, maybe SEELE wanted Mark.06 to be usable while Kaworu had other tasks to do(like keeping an eye on Gendo), maybe they feared that some particular task would present a risk too high for Kaworu, or maybe it was made autonomous just for the fight against the 12th Angel because they knew that they will have to sacrifice it to stop the Angel... we don't know.
Same thing as to how they did it : maybe it was with the Dummy System, or maybe something else(they proved that they had something not needing an entry plug to control the Eva with Mark.09 in 3.0, although that one is very special in its composition)