I believe that the original post mistakenly implies that height SNPs have been replicated. Similarly, IQ SNPs haven't been replicated. Height and IQ have much higher retest correlation and much higher heritability than any big 5 factor. So option 3 is pretty reasonable. Option 2 might be true, but it doesn't help explain the data.
Fitness relevant variation should be hard to detect, because selection is purifying it. If personality is fitness-neutral, then it might be easier to detect.
I forgot about that:
...Take height. Though health and nutrition can affect stature, height is highly heritable: no one thinks that Kareem Abdul-Jabbar just ate more Wheaties growing up than Danny DeVito. Height should therefore be a target-rich area in the search for genes, and in 2007 a genomewide scan of nearly 16,000 people turned up a dozen of them. But these genes collectively accounted for just 2 percent of the variation in height, and a person who had most of the genes was barely an inch taller, on average, than a person who had few of them. If that’
If it's worth saying, but not worth its own post, even in Discussion, it goes here.