Throwing my hat into the ring, I have bought Shovel Knight more times than I'd like to admit. That game has a bunch of version exclusive features, people who bought the PC version won't get to play around with stuff like the amiibo custom knight & crossover bosses that the console versions have. Sure, this is a little different since both versions of this game are on PC, but this is kind of why I'm not disappointed with this decision. Not to mention, Shovel knight is a $40 game at this point that offers a lot less between versions, I bought a bottle of Hershey's chocolate syrup at the store today, and it cost more than what I've collectively paid for both versions of this game.
All of that said, I do think the Itch.io version should be outright delisted or covered with disclaimers and links to the steam page once the multiplayer update comes out. That is a big exciting feature that will get people flocking to this game, make sure they don't get the wrong version.