If in fact the test was the WRAT-4, they really were not allowed to give him more than the 15 minutes allowed. Doing so would break standardization, and invalidate the test. Actually, giving him a scribe was already a violation of standardization procedures. The WRAT is not like the ITBS, SAT/10, or MAP. It's more like a screening version of an individualized achievement test--more on the lines of a WIAT or WJ-lite.
The reason for this strict adherence to standardized administration is that this kind of testing is also used to establish the need for scribe/extended time in special ed situations. Years ago, I received a report written by an outside evaluator that claimed the child needed a calculator accommodation, based on their performance on the WIAT numerical operations subtest--administered with the use of a calculator! Doing so made the standard scores completely meaningless, and actually prevented me from being able to assess the child properly, to document that a calculation disability was present (since it was too recent to re-test with the same instrument).
As to how this will affect his outcomes in this case, I would not be too worried. There are 40 items, yes, but they are scaled in increasing difficulty from kindergarten to 12th grade level.
And if he receives extended time on the SCAT, that will help to demonstrate that it is a speed rather than accuracy that may have lowered his score on the WRAT. If need be, perhaps you could request that he be additionally evaluated on an untimed calculation test with psychometric properties at least as good as the WRAT, such as the WJ, WIAT, or KTEA.
