Maybe it means installation via Itch application? For instance, I always play Itch games this way, and they're really downloaded on my PC, even if they're HTML5.
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Thanks Adoru. I was also wondering about this myself. With a bit of skullduggery, it is possible to download the games, but not in a way that you would expect itch.io to record it as a download. I think Adoru's answer may be the reason for the download count. I must look into this itch.io application.