It doesn't matter. You come out the same. You are not losing money.
Either way, money that goes into the HSA is not taxed.
If it's pre-tax money taken out of your pay, it's not taxed, but you don't get a deduction for it because it's already not taxed.
If it's after-tax money, you get a deduction for it on your tax return, so you don't pay tax on it. You are calling it "already taxed," but it's not really already taxed. It was included in the taxable income on your W-2, but the deduction on your tax return takes it out of your taxable income, so in the end you are not paying tax on it.
