Itch.io only keeps the percentage you set in your preferences. But since they send you the money via PayPal, the latter applies their own fees. Which, as you've noticed, include a fixed portion. That's only like 30 cents, but it's going to be very noticeable when taken out of one dollar (the percentage they take on top of that is reasonable).
The solution is to let more money accumulate before requesting a payout. You'll also lighten the workload of transaction reviewers, which means the money will be transferred faster.