Do banks charge an extra fee to activate Pix on debit accounts, is that allowed?

No, it's not allowed. The Central Bank prohibits charging fees to activate Pix on checking or savings accounts, whether on debit or any other basic service. If your bank is charging you for that, it's against the rules and you can file a complaint with the Central Bank (they have their own portal) or with the bank's ombudsman. They're required to refund the money.