In Joseph Benson's commentary on Romans 9, he explains that Paul's refutation of the Jews argument that God's word failed is twofold. Paul deals with national election and also with justification by faith. Benson explains the allegorical sense and justification by faith: "In quoting these words, in Isaac shall thy seed be called, and inferring therefrom that the children of the promise shall be counted for the seed, the apostle does not intend to give the literal sense of the words, but the typical only; and by his interpretation signifies that they were spoken by God in a typical and allegorical, as well as in a literal sense, and that God there declared his counsel concerning those persons whom he purposed to own as his children, and make partakers of the blessings of righteousness and salvation. As if he had said, This is a clear type of things to come; showing us, that in all succeeding generations, not the lineal descendants of Abraham, but they to whom the promise is made, that is, believers, are the true children of God.
Benson also explains the literal sense and national election. He does a good job at explain how national election squares with the question of did God's word fail. It may seem like national election would result in the Jews being saved, which would undermine Paul's point. So why reference the election of Jacob? Benson explains: "And his intent herein, as appears from verses 30-33, (which passage is a key to the whole chapter,) is evidently to show, that as God before chose Jacob, who represented the Jews, and admitted him and his posterity to peculiar privileges, above the Gentiles, without any merit in him or them to deserve it; so now, (the Jews through their unbelief having rejected the Messiah, and being justly therefore themselves rejected of God,) he had chosen the Gentiles, represented by Esau, to be his peculiar people; according to the prediction of Hosea, I fill call them my people, &c., cited verse 25, where see the note; and that without any thing on their part to deserve this favour. It was entirely free with respect both to them and Jacob, Cod's mercy and goodness preventing, not the endeavour only, but even the will of both. As, before Jacob either willed or strove for it, the blessing was designed of God for him; so, before ever the Gentiles sought after God, the blessings of Christ's kingdom were designed for them. Yet it does not follow that all who are called Christians, and enjoy outward church privileges, shall be finally saved, any more than it is to be concluded that all the Jews were saved before Christ came in the flesh, on account of their privileges." In other words, explaining that national election doesn't guarantee salvation is responsive to the Jews argument that the word of God failed.