Clarification: Was he tested by a PT or an OT? PTs generally don't deal with fine motor or visual integration. Gross motor is their area.
If he has dyslexia/dysgraphia, it is very likely that it is being masked at this point in his development, because of the shallowness of grade-level expectations, and his high cognitive capacity for compensation. If I recall, you also said you worked with him using a structured phonics-based program (TBT, All About Reading?) on reading, which would be the beginning stages of a dyslexia remediation/intervention, which might also mask an LD as far as scores go. If something like a CTOPP or PAL-II has not been administered, I would suggest that that should figure into the next round of testing, as they are more sensitive to the specific processing deficits of dyslexia/dysgraphia than standard cognitive and achievement batteries are. And if they were done, some more subtest analysis may be in order,to look for compensated dyslexic profiles.
He was tested by PT, not OT. She suggested dyspraxia as a diagnosis consideration which was rejected by ed psych (who stated she was comfortable/familiar with diagnosis).
He did have a CTOPP administered for dyslexia. We used to use AAR but have now abandoned it for explode the code as AAR tended to be too tedious with the reading lists. I also teach phonics on the go (as we come across words that have a new phonics rule I teach them (-ight, -ice, etc), instead of a certain order. I try to let him read books to me that he knows the rules of decoding with, but don't always find easy readers easily. The school has an "integrated method", which allows reading based on pictures and guessing words after decoding the first and last letters, context clues, etc. But DS tends to just randomly guess words if there are too many picture clues and not enough phonics rules.
