This is not the same cross previously seen in 1.0 and 2.0. It is far, far bigger. Recall the scene where Mark.09 goes into hiding from Mari's sniper fire:
Mark.09 is able to hide its entire body under just the upper arm with ample room to spare. You can see the corner where the arms connect near the bottom of the image. We thought this was just a scaling error at first, but it's not. The cross is consistently huge in each shot it's in. In most shots we only have the skulls for scale. You can see them in both of the previous images I included. Those skulls are about the same size as an Eva's head. You can compare the falling skulls to Mark.09's neck stump, and here you can see Unit 13 walking among them to get a better idea of their scale:
We know for sure that Lilith was not that big in either of the previous movies because we have the Spear of Longinus stabbed in her chest for scale:
Lilith is roughly the same height as an Eva, though her torso and arms are considerably more bulky. Her arms would *never* reach the nails embedded in this other bigger cross. The nails themselves are nearly as tall as an Eva. Neither of these images is exactly to scale, but I attempted to add the hiding Mark.09 into the wide shot of the cross to give a better idea of just how massive this thing is. Wozzed was also kind enough to pose a model of Mark.06 on the cross for me as well. Take a look:
Just look at how big Mark.06 is compared to the skulls around it, and it's still too small to actually fit on that cross. Its hands can't even reach the nails! There's another curious detail about this cross too. On Lilith's original cross, there's a horizontal notch behind her head. It's right above the point where the arms connect:
On this other cross, the notch is higher up on the upper arm of the cross. You can see it here:
So what does this all mean? Well, as far as we can guess, it means that at some point between the end of 2.0 and 3rd Impact, Lilith grew to a colossal size and had to be re-crucified on a much bigger cross. This might also explain the discrepancies between her chamber as seen in the first two movies and 3.0: She got so big they had to transfer her to another room. A room like the chamber of skulls did exist in NGE. It's the sea with the pillars of salt where Units 01 and 02 crash down after exiting the main shaft in episode 24. Not a 1:1 direct parallel, but not entirely different either:
Getting into more speculative territory, we think the best time for this to happen was during the credits portion of Evangelion 2.22, during the time that Unit 01 became a radiant giant and it being stopped by Eva Mark.06. There's a quick cut away to Lilith (using a recycled pan and close-up from 1.0) right as Rei starts to enter Unit 01, showing that seemingly nothing is going on with her. Only time you see her in the entire film. This would be achieved as a result of her soul (presumed to be residing within Rei 2) merging with Unit 01 (an Adam) and it having some kind of resonant effect that feeds back into her body.
Despite being impaled on the Spear of Longinus, Lilith's body is not entirely inert. The little legs jutting out of the tumorous masses where her legs should be are constantly in motion, swaying and kicking. You can also see this in 3.0, as her body starts to let off steam and begins bleeding from the eye sockets as the chaos in Central Dogma heats up. The corpse seen here is impaled on two Spears rather than just the one.
3.0 is also where the idea of a link between the various parts of Lilith's body stems from. Her severed head and body are in completely different parts of headquarters, easily a mile apart or more, yet they both begin to react at exactly the same time. Not only that, but when Shinji pulls the spears out, the head bursts just like the body does. As the 12th Angel bathes in Lilith's blood, it begins to transform not into Lilith's original form, but into a giant Rei head like the one that had just exploded. Inside the giant core-head-fetus-Angel thing that encases Unit 13, there are dozens and dozens of smaller giggling Rei heads. They're hard to see because they're entirely core red, but if you look very closely you can see them, and you can hear them giggling throughout the scene where Kaworu laments becoming the 13th Angel:
A similar phenomenon is witnessed when Unit 01 rips open the 10th Angel's core in order to retrieve Rei. Tiny little Reis made of core begin bubbling up out of the core beneath Unit 01's palm:
The 10th Angel's core houses both the core of Unit 00 and the soul of Rei within, so it makes sense that this could happen. Rei is in there. It's not quite so understandable when it happens to Lilith. As far as we know, Rei never joined with her body. Mark.06 was said to be modified so that it functions autonomously, so no pilot would be needed. People have theorized that the 12th Angel ate an Eva piloted by one of the Ayanamis before joining with Lilith and Mark.06, but there's not really any evidence of said Eva existing. It's absolutely possible, but there's nothing concrete to support it, I think.
Given the timing of when Lilith's change would have needed to happen, I personally think it makes the most sense for her metamorphosis to have happened as a result of Rei merging with Unit 01 and the subsequent awakening. If Lilith's entire growth was the result of Third Impact, there'd be no need for the second cross at all. She'd be dead from the damage she suffered and skewered with the twin Spears of Longinus as a headless, bloated corpse that's far too big to fit on either cross.
Lilith having an initial growth phase could also provide a possible explanation for the weird state of the head left behind in the command center. As you can see, it has grown to a huge size:
Don't let the headless Evas below her fool you. They're not even close to being full-sized Evas. If you compare them to the little Gendo standing on the highest platform of the bridge in the first image, they look to be roughly 15-20 meters tall. The best comparison I can find is from the scene in 2.0 where Unit 01 and the 10th Angel fight inside command:
Comparing the two command towers, it looks like Lilith's head smaller than both the 10th Angel and Unit 01, though not significantly so. This means that the head is far smaller than the body left in Central Dogma. Unit 13 can easily climb up her body like she's a mountain with plenty of room to spare. However, if you look at the comparison images I made earlier in the post, with Mark.09 hiding under the cross and the Mark.06 model, her head looks like it'd be just about the perfect size for a body scaled to fit on that cross.
Mark.06 faces a similar problem. The giant white version of it jutting out from Lilith's neck is several times bigger than it should be, but it's still absolutely puny compared to the body it's emerging from. If Mark.06 fused with her while she was already huge and then continued growing after being assimilated, it'd nicely explain the size discrepancies.
I feel like this discovery helps clear up at least a few of the mysteries concerning the events of Third Impact.