Here is a photo of the bow of the sister ship SS PIERRE L'ENFANT, Hull #1001, taken July 12, 1943. She was launched June 11, two days before the COLLIER. One can clearly see the forward 20mm gun.
Here is a shot of the SS JAMES R RANDALL, Hull #979, taken June 21, 1943. She was launched May 2. Same 20mm gun forward.
It must be that the shipyard, Bethlehem-Fairfield, was short of the 3" guns.