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You're right. There was no warning that I had noticed, but, I imagine it would be written somewhere on the site or the terms though. 

I believe/think? the reason that the site permits it, is because the developer payout is still what is being advertised, while the itch.io fee is sort of a tax on top and is being displayed as its own separate warning before the player purchases the game.

Yeah, but in any case (above the $1 minimum) as users we can just pay the minimum amount the developer specifies. We're not forced to always enter minimum+$0.25.