So have you gone through similar lists for dysgraphia and dyslexia and developmental co-ordination disorder? So many of these lists overlap. I am still going with "paediatrician didn't decide, neurologically odd son"... I'm not really suggesting PDD-NOS, but while I am no expert on dyscalculia I look at that list and I think all the stuff you've highlighted is too easily applicable to other conditions too. But pretty much all of it could be down to major visual problems weirdly overcome by a PG child - causing some quirks in other areas of development along the way as he tries to compensate.
Ideal auditory development is reliant on ideal development of the other senses too (surely?). I know blind people are supposed to be able to develop more acute hearing etc, but one wonders if whatever causes a visual processing difference (in the presence of "normal" vision) prevents a straightforward compensation via another sense.
My DD with CAPD, when tested at 7 by the OT for global sensory development had highly, highly developed visual skills in some areas (compensating for auditory weakness), most glaringly her visual speed was about 5 times her auditory speed (pressing a button in response to visual or auditory input), her visual was well above average, her auditory way below. So she definitely was stronger in some ways visually, compensating for the auditory deficit, BUT she also had some particular visual deficits, which I am guessing were either areas that needed better auditory skills to develop normally OR were impacted by the same root causes as the auditory issues... The OT got to the end of the visual tests and said "I can tell from these tests that she's amazing at Where's Wally and cant read."