Their reply makes no sense to me. If they prepare a Form 1099-R, they are obligated to prepare it accurately. For a direct In-plan Roth Rollover that means a code-G Form 1099-R showing either the correct taxable amount in box 2a or leaving box 2a blank and marking box 2b Taxable amount not determined.
To get correct treatment in TurboTax, you'll either need to enter the correct taxable amount in box 2a or leave box 2a blank and mark box 2b Taxable amount not determined. Since that disagrees with the Form 1099-R provided by E*TRADE, it probably makes sense to do it as a substitute Form 1099-R which would preclude e-filing.
