They did. Here is a pic of a '65 Dart.
The wagons didn't rank high when it came to retooling.
First of all they have the round rear wheel openings that all cars were meant to have. The fenders were redesigned in the last second but it was found to expensive to retool for the low volume wagon bodies..
As seen very clearly in this picture all wagons also have the provision for the '63 tail lights in the body, just filled in but very visible.
Using the Valiant body including rear bumper (because of the curve in the fender) on the Dart was also a cost cutting move.