So i have the same situation as the OP. I can do as you say, add an additional payment, but then 1040 line 31 is overstated by the additional payment amount. That amounts comes from Sch 3 line 10 "Amount paid with request for extension to file". This seems like a clear bug in the software to me. I don't see how it isn't. I have to not put an inaccurate amount on line 10 of Sch 3 to account for the amount I added to 1040 line 26.
