The ones that count towards age-related expectations are the maths test, the reading test and the writing teacher assessment.
The maths, science and reading teacher assessment, as well as the grammar and spelling test, don't carry the same weight but give a bit of a steer to secondary schools. However, secondaries will do their own assessments.
In reading, the judgments match. The grammar, punctuation and spelling test is easier to pass than the writing assessment so this sounds right.
The only main discrepancy is maths but the teacher assessments are against the interim assessment framework which is 8 specific areas; the test is much broader. It's possible, for example, that your son isn't strong on using formulae which were worth very few marks in the test but is one of the 8 skills that he must be secure on in the TA.
At any rate, you're never going to get a perfect match between teacher assessment and test results and especially this year where the decision on the pass mark and the scale scores were made after the test. My TAs were very slightly lower than my test results but if the scale had been moved so that my 100s became 99s, I would have been too generous.
I suggest you ask for the scale scores and also which parts of the standard he hasn't met for maths and writing (although presumably this is written in the report?).