This isn't a current uniform thing, but I finally figured out why the numbers on our 1996 uniforms were different.
They were transitioning from Wilson to Reebok in the offseason after the 1995 season. Since you have to prepare in advance for a uniform redesign, Wilson had been preparing the numbers for the new jerseys the year before, so the 49ers had all the pre-made Wilson numbers, in Wilsons own style, ready to go. Reebok ended up winning the contract for 1996-98, but since the 49ers already had the Wilson (rounded) numbers, they used those.
Towards the middle of the season as jerseys needed replacing, or new players were added, the boxy Reebok numbers started getting mixed in with the others. By the end of the year and playoffs, most players had the Reebok numbers.