I definitely picked up on the fact that the Anti-Universe represents the border between fiction and reality - and even that the Godlike “people who were not human” who sent the angels and the spears to Earth may have been in fact the authors of Evangelion itself. But in my post-win evageeks trawl I found an interesting interpretation that certainly deserves acknowledgement on this blog:

Blockio: […] the events in the negative universe are from an elevated state of consciousness, that they have transcended their own reality and are looking from the top down into different ones (in a similar fashion to how EoE Instrumentality transcends reality and looks into different ones). On a meta/multiverse level, the different versions of Eva are connected, but the timelines are seperate.

I’m personally inclined to disagree that the films are on a totally separate timeline from the anime, since to me the Impact events are more about resetting physical evolution and growth (being instigated by fruits of Life and Knowledge) than literally reversing time itself, but there is certainly some merit to viewing the Anti-Universe sequence as the characters literally looking upon the Evangelion franchise as ascended characters.