Although in my opinion is isn't in a great spot (the 1040 Wks, right above the line for the deferral), there *IS* a line in ProSeries to indicate how much SE tax to defer.

ProSeries did force you to enter the amount of profit from March 27th to December 31st on Schedule SE, under a section clearly marked as deferral of SE taxes, so you should have been aware of what it was doing.

Unfortunately, it was a mistake on your part that you missed that Schedule 3 showed the deferral, and that the return was $3000+ short on tax.