While I agree that it's a bit strange, this is just how GTCE works. Particularly for these basic metals I'm not too worried about it, as players tend to just smelt the ore directly or at most crush it before smelting in the early game, and you get infinite basic metal ingots from DML before you even have access to good ore processing.

Did some testing.
The unmodified GregTech .jar has it such that both dusts smelt into three nuggets.
Did some digging and found the change is in the Earlygame script.
The lines hadn't been touched since the original Nomifactory commit so I don't have a clue behind the original intentions.

This change was likely made by Damien (the author of Omnifactory) well before Exa had worked on Omnifactory (now Nomifactory) so that it's easier to acquire iron for early game before DML.

I believe that to be the case yes. I can see just above that it looks like an attempt was made to make Chalcopyrite dust give a full ingot, but unlike with Pyrite the original furnace recipe that outputs two nuggets was not removed so the addition silently(?) fails.