"the benefits of keeping the non-deductible money in a separate Roth IRA are less than they would be for someone who hasn't mingled their funds."
Perhaps that statement is not worded in a way that conveys what you meant to say. The benefits of having money in a Roth IRA are independent of what one has in other retirement accounts. If one has to choose between making an ordinary nondeductible traditional IRA contribution and an ordinary Roth IRA contribution, the Roth IRA contribution is always a better choice regardless of what one has in other retirement accounts.
