I've seen this happen with multiple games. Basically, when managing uploads to Itch, there is a list of checkboxes for compatibility. You are supposed to click the boxes for ALL compatible systems for the uploaded file. This means you have to click the box for both Windows and Linux when uploading the file to Itch.
Most Linux Machines will simply use Wine64 or something, which allows Windows games to be played on Linux, albeit to a degree. It depends how the game is made. If it's made in RPGMaker, there will be missing fonts/text and whatnot, but it should still function. If it's made in Ren'py, there shouldn't be any issues. Unity is able make both the Windows and Linux executables.
But if there is a Working Linux Port, I would suggest adding it via .zip.