I too agree with you keeping in view the Pakistani biking culture.
Actually from 1960 to 1975, there were no standard at all for 2 wheelers. Few companies put gear shifter on left side, few put on right side. Few had pattern N12345(6) and few had 1N2345(6). Afterwards in 1975, USA restricts that all imported bikes should have the 1N2345(6) (as research proved that it helps you avoid accidents) and this standard took approx 5 years to become popular worldwide.
Since 1980s, all international bikes have shift pattern 1N2345(6). If you remember 1990s kawasaki bikes here in Pakistan, they had the same shift pattern i.e. 1N2345(6)
One reason that I can think of 1N2345 pattern in YBR is that Yamaha have plans to export this bike to other countries. This is just a hunch of mine thus it makes YBR an international model.
I found this in the pursuit of finding reasoning behind 1N2345(6) shifting pattern and I still have no opinion which one is superior or natural to use.
PS: I'm still looking for a approved USA research thesis on this where they proved that its easier to avoid accidents and it feel natural on 2 wheelers and there are several posts on internet that says the same philosophy.