Hmm, maybe I know what might have happened, but I don't think I explained how it works properly. You created the zip file by transforming "Your Projects" into an ISO, right? Well, then, you would compress the files in it, transforming them into just one zip file and then trying to upload them to the site again. Answering your question, yes, the engine has both 2D and 3D to make games. At the moment, the V4 I mentioned is in development, which is the version in which they are focused more on 3D. There are some versions that they publish of V4, sometimes very stable. For now, I recommend a more or less stable version with an updated README, but you can take a look at the others.
(README V4)
https://github.com/DanielSant0s/AthenaEnv/tree/v4?tab=readme-ov-file
(somewhat stable version)
https://github.com/DanielSant0s/AthenaEnv/actions/runs/15842346043
(versions)