Isn't it always?Ok so even though he's paying the VAT, it's actually added to his account as credit and not deducted from his payment like it normally would be?
I think you are overthinking this.
When someone pays you a service/product, the total value includes VAT, and is treated as part of the "cost value", it´s not separate, nor it should be from the point of view of the customer.
It´s not the customer fault that the state wants a cut on every transaction, it´s not the customer burden to account, report and pay the VAT to the state.
You gotta think about it like this. Whenever your business gets money, the state gets a cut. The only diference with prepayment is in accounting, the document needs to be processed as a prepayment and later on when you supply the service/product you must refer in that invoice that the ammount that had been prepayed was used to pay that invoice tottaly or partially.
Maybe a simplier way to explain is this. Your customer only paid once (the prepayment transacton), not twice, and VAT only applies to money transactions.