from what i can tell while a penalty amount will appear on the 1040, in TT it does not appear on the 1040-X. suppress the 2210 or leave it. on the 1040-x on the area between lines 17 and 18 make sure that it reflects the overpayment without the penalties
or if you owed, make sure the area between lines 15 and 16 reflects the payment without the penalty.
by the way, the 2210 penalty only reflects an underpayment of estimated tax penalty through 4/15/19. it does not include any late filing or late payment penalties if they apply
