OP.
Attainment and Progress are two separate things.
My y9 DD2 has apparently made 'Excellent' progress in PE since starting secondary. However they are saying she is 'on track' to get GCSE grade 2 if she were to select it for GCSE. This is not surprising as her motor skills were assessed as bottom 1%.
So your DS can be making excellent progress compared with his SATs, but still have low attainment. So he has made 'excellent' progress, but still only 'securing' the relevant knowledge according to the general y7 expectations.
re Maths in particular - are you sure they aren't set? Most schools set for maths quite early even if they don't set for anything else in y7.
DD gets awards for Progress in subjects, and at her school you can get credits for general stuff and so be 'top of the class' for credits. Both of these can happen even if you are bottom of the class for attainment.
In your situation I would focus on:
attitude - does the school say he's trying
progress - does he feel he is learning stuff and improving, and does the school think so too.
I would only flag with the school right now if your son says he is lost in lessons as doesn't understand, or bored in lessons as too easy. You may find you get more helpful reports in terms of absolute levels at the end of this term or end y7.
(And yes, nothing to do with primary now)