Can I make a web game where you can download the Window version from downloads ?

Depends what you mean by windows version. If you need a browser to play your game, then no. Else, potentially yes.

I thought about the same thing: I could upload the HTML export of my TIC-80 game to make it easier to play, providing Linux and Windows exports as well of course. Maybe it goes against the rules, but it would be pretty convenient.

As long as your game is either a windows or ubuntu game, it's fine. When you submit, you'll be asked to indicate if your game is for windows or ubuntu --- other platforms won't count.