For NGE 2's production, I understand that the Classified Information sections were based on a 10 hour long interview with Anno, but the rest of the game was not (including all of the endings).

So is nothing really canon to NGE/EOE except for the CI?

As far as I'm concerned, the meaning of "canon" is different in Japan. They care more about the "officiality" of the product than the "canonicity" of its story. If a product is licensed and endorsed by its owners, then it's good, even if it's not part of what we consider to be the "main narrative".
NGE2 is not canon to NGE, obviously. It's fundamentally different from the show and even the CI contains some questionable information. But it's an official product nonetheless.

I have looked into this myself for the wiki articles significantly, you can in fact see a rundown on it here. Basically, while the game devs had access to some Gainax docs and all, and did interview Anno and other staff, they very clearly state how what they depict in the game is basically their own version of it all, and the game itself is very much an open-ended RPG. The FAR, notably, were present in early plans for the anime but they more or less decided to not directly address them in NGE itself, then it slowly returns to canonicity. They have extensive development logs on their site, which are not translated but have been archived: https://web.archive.org/web/20040209123 ... /info.html