You do have Roth IRAs, so I probably would not have unmarked the Roth IRA box, you just don't have any contributions that would be entered under Deductions & Credits.
TurboTax records your basis on the IRA Information Worksheet. The rollover to a Roth IRA of the after-tax money from traditional account in the 401(k) is treated the same as nontaxable Roth conversions from a traditional IRA, so it adds to nontaxable conversion basis for the year of the rollover. The reason that TurboTax asks if the distribution was rolled over to a Roth IRA is so that TurboTax can track the basis correctly. (Check to see that TurboTax didn't somehow erase your Roth basis information when you unmarked the Roth IRA checkbox under Deductions & Credits.)
TurboTax forces you to split the Form 1099-R so that the questioning needed to determine what happened with what dollars doesn't get overly complex. Although it would be extremely unusual and I've never seen a post mentioning this happening, you could see combined a single Form 1099-R from a traditional 401(k) account a rollover to another traditional 401(k) or IRA account, an In-plan Roth Rollover and a rollover to a Roth IRA, in which case the original for would need to be split into three forms for everything to get recorded appropriately.
