I'm still not sure I completely understand what you're saying (screenshot would help), but I can explain why the Itch.io cut and fees work the way they do (someone from Itch please correct me if I'm wrong about any of this). Itch, as you know, allows you to share any amount from 0% to 100% of your revenue with the company. That pays for website hosting, development, support staff, etc. In addition to those costs, Itch incurs fees from payment processors like Stripe and PayPal both when they process initial payments, and when they send the final payout amount to you. Those costs are passed on to you regardless of what your Itch cut percentage is set to. If you set up your own website and dealt with PayPal and Stripe directly, you'd pay those exact same fees. None of it goes to Itch.
Other stores like Steam don't list those fees separately, but they still exist, they're just hidden in the much larger (typically 30%) cut that the store takes. If you set your Itch cut to 0%, Itch.io will make no money off of the sales of your game, and in fact will lose money paying for the hosting of your game's files and such. Itch is nice enough to do that stuff for free, and I'm not saying that you shouldn't take them up on that offer, but it's worth understanding what those different line items on your payouts mean and where they really go. Personally I think processing VAT, fraud prevention, refunds/support, hosting, analytics, etc. is worth at least a few bucks, but the nice thing about a pay-what-you-want model is that you can make up your own mind.