Based on the track, he clearly has no intention of entering Class-D at 1,000ft or below as he'd have to turn 45 degrees left, a long way off track and may be over solid cloud at this time.
He has Class D in the step ahead of him. I suspect the GPS didn't give an easy indication of the exact altitudes of the steps, just that they were there.
I think the Class D in front of him, on track was what he thought he had been told to transit at or below 1000'.