It's not unknown for two routes to be suggested. Some riders prefer quite roads, others don't mind traffic.
The quiet route is generally shorter, but slower because it's on minor roads. As long as the distance can't be reduced by short-cutting it fulfils the criteria of Audax. The controls are waypoints and it's accepted that it would not be feasible to define all the routes, or to enforce a single route.
It might matter more if the times were published, as you wouldn't be comparing like with like. But as long as the minimum distance is done within the appropriate times it's not a problem.
