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I think this means you can fix it just by taking the files you had in the appimage and zip them up as is. 
The user always need to give the binary file execute privileges though, standard fare on Linux so that's how it should be, just make sure to mention somewhere, in the readme or on the itch page, that it's in the bin folder. I am used to finding it in the applications root directory.

Even if a valid point. AppImage is a very handy way of shipping software :*