I think this might be where you are confused: "Form 8959 show the calculation and but did not reconcile and apply only the difference, if any, to line 25 c. ..... It went ahead apply the full 0.9% additional tax to Form 1040. That means we add extra and not necessary amount for the tax due."

It did not apply only the difference because line 25c is for amount withheld. It is for Payments made and not Tax computed. From: https://www.irs.gov/instructions/i1040gi

"If you had Additional Medicare Tax withheld, include the amount shown on Form 8959, line 24, in the total on line 25c. Attach Form 8959."

The tax computed will come from Schedule 2, line 11, to the 1040 Line 23.

Line 24 is Total tax.

Line 33 is total payments, credits, withholdings, etc.

Hope that helps.