Both my PowerShell and Windows Explorer builds have "AKnightEternal" as the top-level folder inside the archive, and the path to the index.html file is the same in both - AKnightEternal\www\index.html. Itch just can't find it there in the PowerShell version for some reason.
I'll give the changes you suggested a try when I get a chance, although I may wait until the game jam I've submitted this to is finished with judging since I've already got the Windows Explorer version of the zip uploaded and working.