When you enter a code-G Form 1099-R that has $0 in box 2a and indicate that it was rolled over to a Roth 401(k) or Roth 403(b), that's the end of anything having to do with the Form 1099-R. The only thing that TurboTax does with this information is include on Form 1040 line 5a the amount from box 1 of the Form 1099-R and exclude it from line 5b with the ROLLOVER notation. Nothing about a Form 1099-R indicates the years for which the contributions being rolled over were made, so it's impossible for TurboTax to infer anything about excess contributions from the entry of the Form 1099-R.
"My core issue is when I enter in this 1099-R information in TurboTax, it ultimately leads to a page where Turbotax cautions me that i've contributed more than the allowed amount to 401k during the year and that i may be subject to penalties, etc.'
Exactly what is TurboTax saying? Excess contributions to a 401(k) cannot result in any penalties (only additional future ordinary income taxes), so perhaps you are mistakenly entering these contributions as IRA contributions and TurboTax is noting that you made an excess IRA contribution that is subject to penalty. Make sure that you are not entering anything about this anywhere under Deductions & Credits. A 401(k) is not an IRA. Enter amounts shown in box 12 of your W-2 only in box 12 of TurboTax's W-2 form, nowhere else in TurboTax.
