'The flight crew looked out the right window of the flight deck and identified the traffic to their right and high against the skyline. The traffic appeared to them to be stationary in the windscreen relative to their own aircraft and with a high closure rate (from TCAS data the aircraft were 1.25 NM apart at the time of the TA alert)'
So the report does mention a visual confirmation.
At this point the TCAS showed the GA-8 as doing 240 knots, so I think the position data is suspect. The GA-8 pilot estimated the distance as 2 miles. If you use a more reasonable 120 kt for the GA-8 it adds 1/2 a mile i.e. 1.75 miles.
The GA-8 was also 500-600 feet higher. 2 miles and 500 feet doesn't seem like something to worry about with visual separation.
It was shown to pass 200' above ZPJ
This is where there is no visual confirmation. This was 40 seconds later, the jet has turned 90 degrees, and the GA-8 has somehow averaged 200 knots to get to this position. I'm sure the altitude is right, but it seems more likely that XGA was still at least a couple of miles away horizontally.