The comment about it being "single entry" only happens after Asuka has injected the angel blood into her Evangelion and removed her hex pillar. The terminal signal plug that she intended to plunge into it was blocked when New Eva-02's AT Field activated. Asuka rears back, ready to strike, and then we get line 1378, 「シングルエントリーじゃなかったの?」I hate lines like this because you never know if they're literal ("It wasn't single-entry?!") or rhetorical ("It was single-entry, wasn't it?!") I know Unit 13 is referred to as having a Double-entry System, but I'm not sure if "single-entry" is meant to imply that Asuka thinks it only takes one plug, or that it only has one plug currently inside it. As we say, the former reading wouldn't make much contextual sense-- how could Wille not know something so crucial about this last Evangelion that they need to destroy? The latter reading might make a bit more sense, since earlier in the film there's a scene between Sakura and Asuka where Sakura mentions that there was data on the DSS choker's data recorder showing that another pilot blew up right in front of Shinji.
Line 889-896:
Sakura: "The operation history of the choker was stored in our MAGI copy. It told us there was another pilot who died right in front of him when it exploded. For him to go through that, and then come back to the Wunder... Why?"
Asuka: "Beats me. I'm more interested in why Captain Katsuragi even gave him permission to come onboard."
Maybe it's a comment on how Asuka thought there was only one dead pilot in Eva 13 who shouldn't have been able to do anything, much less blow her arms off with eye beams and squirm out of its restraints.
Quantum Kaworu. The scene where Original Asuka appears isn't particularly grounded with reality-based imagery, the walls of the entry plug are going a little kooky. If I recall correctly, Quantum Kaworu is standing upright, and has some of the same speed lines around him that we saw after Mari ejected Shinji from Unit 13 in Q. (I could be recalling incorrectly.)
When Shinji and Gendo fight in Tokyo-3, it's meant to be like everything is a scale model, yes. The buildings are scattering and sliding around, and at the end of the fight sequence, Shinji actually falls off the Tokyo-3 "stage" and into a painted backdrop of the sky. The film makes very clear that what they're fighting on isn't real, it's a set inside Shinji's head.