I believe Bridgestone's intent was to provide a distinct separate gear position for neutral when riding in town. On many bikes with neutral a 1/2 stop between 1st and 2nd, neutral is hard to find when stopped, largely due to the remaining friction from wet clutches. This friction loads the gears making it difficult to shift into neutral. You either push too hard and find you have skipped through neutral and on into 2nd or 1st, or not hard enough and you are still in the same gear. With Bridgestones full neutral position, this was never a problem.
Although the direction of the shift pattern is mostly personal familiarity, it always seemed more "natural" to me to have the direction of the up shift be in the direction your foot has the most force, pushing down. When you're running hard and shifting as fast as possible, it's the up-shifts you generally want as quick as possible.
I first learned to ride a BS 90, had some difficulty adapting when I got a Honda 305, and less when I switched back to a BS 350 a couple of years later. By then I was pretty well adapted to whatever I happened to be riding.