ISO639-3 is derived from The Ethnologue. The author of this work have a certain point of view on the definition of "language" (vs. "dialect") with a strong tendency to split languages into smaller units. Note that the authors of the Ethnologue have a open agenda that is different from doing science. Divide and Conquer.
Are the languages spoken in various Arabian countries actually mutually intelligible? If no then it makes more sense to regard them as separate languages.
In China the government likes to officially categorize various Chinese languages as "dialects", but the reality is that the difference is really huge between some of them, e.g. comparing Mandarin and Cantonese is more like comparing Italian with Spanish than American English with British English. Most Mandarin speakers don't understand nor speak Cantonese at all. Therefore there are many language codes for various Chinese languages as well and it makes sense to me.
I wonder whether the situation is similar in Arabic: If you can't even understand some of the Northern African Arabic then how can you claim they're the "same language"? Some people might try to do so politically but linguistically it would be far-fetched. The situation is just fundamentally different from American vs. British English I suppose.