There's no reason why the #1 and #2 cylinders should run the same jetting.

Consider the engine as two 125cc engines as that's what it is. It's two engines linked to a common gearbox.

Unlike most parallel 250cc twins, the NSR (and other V2 engines) do not share the same basic engine configuration between the #1 and #2 cylinders. The crankcases are different in shape and volume and the combustion chambers are different thanks to spark plug offset.

So, apart from running at different temperatures can you now see why they will run different jetting?