You should not expect to see Form 5329 if this is a qualified rollover.

The issuer of the 1099-R issues the code for what they know. They don't always code for a direct transfer, and they won't know about a rollover within the 60 days if your taxpayer did it themselves.

"1) Early distribution (taxpayer is under age 59-1/2) and there is no known exception to the early distribution penalty. Generally file Form 5329, however for a rollover to a traditional IRA of the entire taxable part of the distribution, do not file Form 5329;"

What you confirm is if it met the rollover requirements, including that when a taxpayer gets the money payable to them in between the source and destination, there typically is mandatory flat withholding. Make sure they rolled the gross distribution, not Net (they would have had to make up the withheld amount).

If you have everything that verifies it meets the requirement, then you enter the data accordingly.