Obviously this has nothing to do with Turbotax software.
As a general business proposition, there is no special reason that blocks the the CPA from writing a check for the penalty, have you write a check for the tax, and put them in the same envelope. Or, you could go to www.irs.gov/payments, and make an electronic payment for the amount of the tax, and they make an electronic payment for the interest and penalties.
However, there is no reason that compels them to pay separately, either. It's part of your business arrangement with them.
