For the cost of just a few pennies per day for each $1,000 that is late, use the payroll date. If you're investigated by the DOL, they now can't question the choice regarding the loss date. Using the pay date eliminates that scrutiny.
To me this is one of those rare times logic and retirement law work.
What is the "loss" at issues here? The company is holding plan assets and has a 0% loan from the plan. When did that start to happen? It seems like that has to be pay date. That is the day the cash became a plan asset. So the loss date starts on pay date. The fact you are given a little grace under the rules to get the cash into the plan doesn't change that. So once you are required to decide when did the cash become a plan asset and the 0% loan started I don't see how pay date isn't always the answer.