Madinah as it is in Arabic is said to be mentioned by name in the Qurran four times, Surah 9: 101, 120; 33: 60; 63: 8. And in all for of them the name mentioned is Madinah not Yathrib. Which is significant because Madinah is actually the Arabic word for City (the traditional Islamic narrative is that Muhmmad changed the name of Yathrib to Madinat Rasul Allah, The City of the Messenger of Allah). I looked at all four verses and in each one simply translating Madinah as "The City" still allows the verse to make sense.
I also mentioned in that prior post Sebeos being the oldest historical reference to Muhammad we have. And looking at that account again I noticed something interesting.
Twelve peoples representing all the tribes of the Jews assembled at the city of Edessa. When they saw that the Persian troops had departed leaving the city in peace, they closed the gates and fortified themselves. They refused entry to troops of the Roman lordship. Thus Heraclius, emperor of the Byzantines, gave the order to besiege it. When the Jews realized that they could not militarily resist him, they promised to make peace. Opening the city gates, they went before him, and Heraclius ordered that they should go and stay in their own place. So they departed, taking the road through the desert to Tachkastan Arabia to the sons of Ishmael. The Jews called the Arabs to their aid and familiarized them with the relationship they had through the books of the Old Testament. Although the Arabs were convinced of their close relationship, they were unable to get a consensus from their multitude, for they were divided from each other by religion. In that period a certain one of them, a man of the sons of Ishmael named Mahmed, became prominent. A sermon about the Way of Truth, supposedly at God’s command, was revealed to them, and Mahmed taught them to recognize the God of Abraham, especially since he was informed and knowledgeable about Mosaic history. Because the command had come from on High, he ordered them all to assemble together and to unite in faith. Abandoning the reverence of vain things, they turned toward the living God, who had appeared to their father–Abraham. Mahmed legislated that they were not to eat carrion, not to drink wine, not to speak falsehoods, and not to commit adultery. He said: “God promised that country to Abraham and to his son after him, for eternity. And what had been promised was fulfilled during that time when God loved Israel. Now, however, you are the sons of Abraham, and God shall fulfill the promise made to Abraham and his son on you. Only love the God of Abraham, and go and take the country which God gave to your father Abraham. No one can successfully resist you in war, since God is with you."Scholars see this event as correlating to the event traditional Islamic history knows as the second pledge at al-Aqabah. Except the destination of this joint campaign is the Biblical Holy Land under Roman rule not Mecca, which I feel is consistent with the original "Mecca" being Petra. In this context, the city where this alliance was made I doubt is actually as far south as Yathrib.
What "Arabia" meant in antiquity was often a little broader then we'd define it today. Damascus was considered part of Arabia, in Galatians Paul seems to refer to his time in Damascus as being in Arabia, he also implied the city was under the control of Aretas at the time. Damascus is the city that wound up becoming the civil capital of the Umayyad Caliphate.
But another interesting candidate is Tayma/Tema, an Ishmaelite city that is known to have had a major Jewish popular in Pre-Islamci Arabia. And yet seems missing from the traditional history of Muhammad and the Rashidun Caliphate. It is arguably just as close to Khhyabar as Yathrib is but in the opposite direction. And one of the first places Muhammad sought to conquer after establishing his rule of Medina was Dumah, a location much closer to Tema then it is Medina.
Update: Apparently the name of Yathrib is in Surah 33:13. Which is probably the same name Ptolemy refereed to as Iathrippa.
I think the name of Yathrib might come from Jetur a son of Ishmael. In the past I'd gone along with Jetur being the Iturians, but I now see Yathrib as much closer, but the idea of both being connected isn't impossible. Yathrib seems to have been founded by people who migrated there from further north following the conquests of Nebuchadnezzar.
Upon a closer reading of Surah 33, it's not impossible that Yathrib was being mentioned as a name of a city or tribe that's part of Muhammad "confederacy" (Confederates is the name of the Surah) but not necessarily his base of operations.