Hey. You should use ZIP to compress the linux build too. See http://itch.io/t/11918/rar-support-is-not-happening-repack-your-games.
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Got the same info from the official client's devs https://github.com/itchio/itch/issues/183#issuecomment-165986223
So sorry about that. The linux version should be uploaded now as a .zip file.