How to add paypal service charge fee to user defined amount payment type

this feature does not work with a "user defined amount

That is correct. Since it is already on the user what amount will be inputted, the option for service charge is no longer built-in within the payment type.

To achieve the version that has defined amount + service charge fee, you can do it instead using custom amount payment form.

You can use the regular fields instead to calculate all the amount (regular amount + service charge fee) and then pass the total amount value to the Payment field (user define amount).

You can check this user guide: How-to-Pass-a-Calculation-to-a-Payment-Field

Let us know if you need further assistance.