I think that the IRS Automated Underreporter System only checks the amounts reported on the tax return's forms and schedules. TurboTax-required splitting of a single Form 1099-R reporting rollovers from a qualified retirement plan with some going to a traditional IRA and some going to a Roth IRA doesn't seem to present problems, so I doubt that there would be a problem splitting a code 3 Form 1099-R.
