Line 4 on the 4868 asks "Estimate of total tax liability for 2016". Line 5 asks "Total 2016 payments......". line 6 asks "Balance due. Subtract line 5 from line 4".
If you have already done the first pass and know that you are receiving a refund, all that matters is that line 6 is zero (as it should be if you expect to get a refund). This means that you won't send any money to the IRS when you file the extension.
I can't see the TurboTax amendment dialogue in my tests, but this is the result that you want.
Worst case, just go to the IRS website and form-fill the 4868 and print and mail it.
