Yes, the amount in box 5 of the Form 1099-R represents the after-tax basis that was included in that distribution and the amount of basis that transferred to his traditional IRAs if the entire gross amount was rolled over (as long as amount in box 1 is greater than the amount in box 5).
If less than the total gross amount was rolled over, say, because some was withheld for taxes and no other funds were substituted to make up the difference, the portion not rolled came first from basis. However, I'm guessing that the Form 1099-R has code G indicating a direct rollover to the IRA of the entire gross amount.
