Actually, I just found a solution! if you put the lines: 

var url = window.location.href
console.log(url);

inside your index.html file, you can see what itch encodes your url as in the Inspect console. Then, you can append your params to the end of that url and run that. Those params can be read as usual from inside your game.

Example:
Doesn't work: https://lysst.itch.io/examplegame?USER_ID=1234&COND=1
Works: https://html-classic.itch.zone/html/11111111/examplegame_build/index.html?USER_ID=1234&COND=1

Things to note here is that the second link will break if you change the file name (perhaps even when changing out the file for one with the same name - haven't tested it) and it plays the game right in the browser, so you dont get the itch formatting.