This is not an issue ... the W-2 would not show any code W in box 12 naturally since the contribution is not being made thru the payroll system.
You will make the contribution to your HSA outside of a payroll system and deduct it on your return. In the TT program you will just complete the HSA contribution section and the HDHP section ... it is just that simple and will not get you an IRS letter.
The HSA is handled in 3 parts in the TT program :
First the contribution:
https://ttlc.intuit.com/replies/4557768
https://ttlc.intuit.com/replies/4785646
Next the limitations screen to confirm you are eligible to make the contributions:
Until you complete the HSA portion of the TurboTax interview to establish your eligibility for an HSA contribution, TurboTax will treat the amount entered on the W-2 form as an excess HSA contribution.
https://ttlc.intuit.com/replies/4788059
And lastly any distribution:
https://ttlc.intuit.com/replies/4787864
