Just sitting here looking at my copy of The PBY Catalina in Action and most of the shots of the retractable gear PBY's (PBY-5A,-6A, OA-10 and Canso) appear to have the interior of the main gear wells painted black. In fact, the main gear assembly appears to be painted black. There is one picture taken
in 1948 of a Coast Guard PBY-5AG, in which the aircraft is over-all aluminum and the wheel well appears to be aluminum also. To the best of my knowledge, the Navy stuck with zinc chromate as a primer until the early 50s when it changed to the epoxy family of primers. My understanding is that the Navy was dissatisfied with the properties of chromate (zinc chromate greatly retards corosion on aluminum and magnesium but will not block it completly), so they went with epoxy which gives much better protection. They did go to white for the reasons you mention.