No, it is not available in Desktop.

For customers where I know they usually pay via credit card, or if I'm unsure, I add a processing fee per the above to the invoice-- in the description I have typed out in caps "IF PAYING VIA CHECK PLEASE DEDUCT PROCESSING FEE".  Then, when I get a check I delete the fee off the invoice before applying the payment.

Messes with our 'sales' numbers a little as the income is missing if we already closed the month, but it's worked ok.

I really wish they would add this feature for States where it's legal to charge the fee.  I assume they don't because it complicates their compliance process across multiple jurisdictions.