I think we didn't get to see it because it wasn't in the script to be shot. It was in the First Draft of the script, not the Final Draft.
My hunch is that the scene was excised, not because of the contrast his costume would have with the extras or other actors, but because, as interesting as a hat is, it didn't really further the "adventure on Talos IV" narrative of this pilot episode very much. (If they wanted to do the scene, but the hat was just too contrast-y, they could have shot it without the hat. I think the decision to introduce the Captain by having him command the ship on his bridge rather than by dressing down a junior officer at the docking hatch probably wasn't because his hat wouldn't jibe with the skirt and shorts of other characters.)