Here are some of the factors I've considered and come to various hypotheses on the significant overlaps:
* A study showing the IQ is a stronger factor to predicting myopia than occurrence of myopia in parents.
* Cortical thickness studies showing one line for NT IQ, another for MG that follows the NT line but overall thicker, and a curve for HG.
* A study showing a reverse bell curve based on minicolumn size and distribution that shows gifted tend towards either smaller clusters in a denser arrangement or larger clusters in a sparse distibution with long connections. Another study showing a very strong correlation between smaller minicolumn size with denser distribution and autism. Can't remember if study included dyslexia or if that was a speculative connection in Eides book showing dyslexia related to the larger minicolumns in the looser distribution.
* Mass anecdotal clusterings between poorer handwriting and giftedness (even a study showing doctor's handwriting failed to be read by automated handwriting readers vs. other medical workers.)
* Massive anecdotal evidence of overexcitabilities (including allergies) for many gifted kids
* And quite a few other random tidbits, education, and personal experience
Amongst all of these you get many "Useful but insufficient" factors that may contribute towards higher IQs. You also get red herrings and false negatives on some factors (e.g. an EG might internalize early and master overexcitables quickly before they are noted.)
So there's the architecture of the cortex as one key physiological piece. There is also some degree of richer experience (overexcitabilities, something dopamine related?)
And then perhaps some X factors, things that make the brain take on a bit different role. Here's where my pet theory comes in. A huge amount of the brain is at primary an optimized sensory processing machine. The forebrain can coordinate and "takeover" other processing areas. Triggers that make a sensory system unreliable and require a forebrain intervention to prevent fullscale system collapse open a door to intentional control of those areas.
If that door opens, then suddenly that processing system is available to much more than automatic sensory processing. Vision issues, oversaturated emotions, ear infections, an oversaturated sense, allergies, muscular control issues, etc.
Doesn't cover all cases, but fits lots of data I've encountered. But many chicken and eggs with this and just as many bunnies running around trying to hide them.