Isn't the NNAT a non-verbal ability test, like looking at matrices? How did he do on matrix reasoning on the WISC?

It sounds like your district is extremely unreasonable if they won't even look at other test results. I would consider if the program itself is as unaccommodating as the selection process. For instance what happens if he doesn't do well on classroom tests because of anxiety? Do the teachers understand 2e?

Since they did let him re-take the test with extended time, you'll probably have a hard time fighting this. Is this a program where there are a limited number of slots/seats? It seems like those programs end up having the most unreasonable or potentially unfair admissions practices because there has to be a cut-off line somewhere.