1.- It's more complex. If you search in the forum, there are several posts where it is explained in detail and with examples, but basically you must deduct the transaction fee from the payment operator, the Itch percentage, the tax withholding (if applicable) plus refunds or other expenses if applicable.
The value shown is only an estimate, the real value to be received along with the full details of each transaction is calculated when you request your payment.
2.-As long as you don't commit to anything, you shouldn't have any problems.
Be clear with your buyers, look for some examples of disclaimers from other games that can help you.
Usually players understand that buying a game in early access has its risks, but it's best to make that clear in writing, so that no one can claim that you cheated them and you shouldn't have any problems.
3.- Itch does not charge for generating keys, no matter the amount.