Remember that comparing cross section areas only tells you a very limited picture.
(and for those playing at home all you need to do is d1^2/d2^2 - all that pi stuff cancels out... mmm pie)
As you change cross sectional area you are changing the volume of the pipe (doubt there are any infinitesimally small pipes in an engine to stuff that statement up.).
When volume is changes you must still fall true to combined gas law where:
PV/T = constant, or simply P1V1/T1 = P2V2/T2.
since the volume increases (i.e. V2 becomes larger) and temperature would stay constant in the 2 pipes, the pressure in the pipe will have to decrease.
Now is a lower pressure in the pipe a good or a bad thing? I'll leave that one alone.
My thoughts on porting and polishing are to remove any edges, roughness and irregularities in the pipe. Roughness increases fluid friction (bad), step changes form turbulent flows (badish - all depends on the scale of bad) and irregularities are bad too. Essentially in a perfect fit, there would be no flanges, just seamless joins to eliminate all these bad things. At the end of the day they would add up to very small gains, but sometimes those small gains are worthwhile.
A back to back plot of ported vs unported would be awesome if anyone wants to do that
