What is the proper way to publish a game for multiple platforms (e.g. PC/Max/Linux, WebGL, etc)? Do I upload and publish individual versions for each platform?
It depends on how your game was made.
With a traditional language like C, you would ideally compile the project for each platform, and make different packages for each one. For a language like Java, one compiled project can work on multiple platforms.
Ultimately, it’s your decision. Itch allows you to upload one build, and mark it as playable on multiple platforms, or upload different builds and mark one platform on each one.