It sounds like your school has a high cutoff for gifted placement. In our district this would have been more than enough for him to be identified as gifted (I think our cutoff is as low as 89% with three other indicators.)
Whether he made it into the program or not, he's still scoring within the top 5% which is a great range. He's obviously flourishing. If your district is anything like mine, the school will do another testing in 3rd and another in 7th. Your ds was tested quite young. If you see a disparity between these scores and what you're seeing in him down the road, you can always retest him.
That said, if you suspect their testing is inadequate, and a group ability test such as the Co-Gat often is as it underestimates many gifted kids, you may want to dig deeper.
