Trying to answer my own question here:

I remember from some reading somewhere that Form 5498-SA Box 2 is a combined amount contributed by both the Employer and Employee through Payroll deductions and this amount is already pre-tax and does not need to be entered in Form 8889 Line 2.

I also believe that it is only when Employees made contributions from outside of payrolls then the amount is needed to be entered on Form 8889 Line, in order to deduct it from taxable income.

Can someone confirm that this is correct?

Thank you !

Sui