Why did Nissan fold the sequence of intake and exhaust ports in the centre of the head rather than doing a consistent pattern from cylinder 1 to 6: i.e:

E1I1 I2E2 I3E3 | E4I4 E5I5 I6E6

rather than

E1I1 E2I2 E3I3 | E4I4 E5I5 E6I6

Having E3&E4 side-by-side in the middle does not seem like a good thermal geometry.

As well, consistent port and chamber geometry and intake runner and exhaust runner spacing has been sacrificed... I am curious as to why?

I'd guess design and/or production efficiency. This is true for many inline engines. The front and rear cylinders are often mirror images. Was the same on my old MG, and I believe my euro-323i was this way as well.