There IS A SOLUTION to this.  Just posting to be helpful. I have nothing to gain from this, but I figured it out for my own company and thought I'd share:

If you want credit card fees charged to your customer at 3%, and you want that option as an automated thing that happens without any interaction from the user, I have accomplished this via Zapier, fairly easily.  We have the invoice created automatically via Zapier when the sale closes in our CRM, but that isn't necessary.  The 'trigger' can be from a CRM (Zoho, in our case), and it can be automated to create the invoice and the 3% fee line, or the trigger could be the new invoice creation in QBO, and the result could be adding a new line item with the 3% charge.

But we complete the sale in our CRM, and within seconds, the customer exists in QBO, and the invoice is created, with the optional line item adding the 3% credit card fee.  The email template clearly explains to the customer that if they pay with check, to only pay the amount of the sale before the CC fee.  In that event, we just delete the optional fee line and the invoice defaults to 'paid in full'.  

If this interests anyone, I can give more detail as to how to complete this process.  We didn't want to have to manually create the invoice, add the 3% optional fee, or email it.  We just wanted ALL that to happen automagically when the sale is completed in a different application, and after a few hours of tweaking and finding the right features in Zapier, I got it working beautifully.  Just throwing it out there. :)