Usually, win and linux downloads are the same zip file, since theyre more similar in how they run than mac (they're both considered PC). Unless its specifically a seperate download, you're usually good to use the same file for both :)
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Personally, my process is that I download onto the external ssd (which you can do by changing your download destination in your browser settings) and just extract to the default folder it creates. After that you can move the unzipped folder from your downloads to wherever you want it to be :)
Beyond that im not quite sure I understand what the problem is, I dont know how to code 😔 the devs do respond to itch comments though!