I just looked at 15.3 and it does say overriding authority, however it also mentions a clerk and my interpretation is that the director has authority over the clerk rather than authority over the entire set of rules, it clearly states in the same paragraph that the clerk cannot give orders on the following matters without the director's agreement, so to me thats what the authority means.
So in regards to the FIA decision, it doesnt look stupid, as the rules are written badly in a vague way that it can be interpreted in that way, but it is my opinion that was not the original intention when the rules were written.
So given its not clear cut and its open to interpretation then yes I think CAS could easily take a different view.
Here is the quote.