Yes Quran is not a history book. But how are you sure Ayub (as) and Yunus (as) are not part of Bani Israel. It is only because the number goes above 12?
That is part of it, but there is more proof. For example, chronologically, the Quran mentions all destroyed people and cities before Musa (a) and that the Pharaoh and his people are the last of the destroyed people before Mohammad (s) is sent.
So when it talks about this generally, you can deduce for sure Yonus (a) comes before Musa (a). Rationally, it also doesn't make sense, the children of Israel rejected Prophets but weren't destroyed. Why Yonus (a) then sent to a city among them and they are threatened to be destroyed.
When it comes to Messengers (a), there are different types. There are those who if rejected, will result in destruction given some conditions.
Isa (a) despite being rejected, didn't cause children of Israel to be destroyed.
As for Ayub (a), it's yes, he would add to the Twelve beyond that, that refutes it in Quran, but also if you study the book of Job and how it's related, you realize this is a story of someone outside the people of Moses'. None of the people Moses' witnessed this, it's rather, a story related to them, much like Luqman (a) is not of this nation of Mohammad (s) but we learn from him and have a chapter about him.
This is getting silly, it's as if someone wrote a hadith or put lineage that Idris (a) was from Bani-Israel, you would believe it. This doesn't make sense.
Yonus (a) also I mentioned is Greek for "sign of God" while all Anbiya (a) of children of Israel had Hebrew names, and the reason why Yonus (a) doesn't, is because, he is told about by Nabi Isa (a) in GREEK and NOT HEBREW.
But even if all that was not true, and none of this evidence existed that I mentioned, other then what is mentioned of "twelve", then yes, we have to decode Quran in a way there is only Twelve Successors to Musa (a) of his Ahlulbayt (a), because that is how Quran clearly defines it and explains the covenant with respect to Twelve Captains clearly.