We need to distinguish between what is actually a scientific evidence and what is merely a scientific conjecture common in anti-Islamic rhetoric for which there is no scientific backing.
Regarding the parts that Mecca was non-existent at that time, Muhammad (sws) not being Arab and similar points–they all lack scientific evidence and if you dissect deeper, are merely based on conjectures and fueled by anti-Islamic rhetoric. These points are so absurd they are not even brought-up by mainstream Atheists who are scientist themselves like Richard Dawkins, P.Z. Meyers, Lawrence Krauss, Daniel Dennett etc. etc. Finally, all these conjectures go against the most reliable source of knowledge i.e. established history which is transmitted through ijma and tawatur. If someone starts denying that part of knowledge, then its better to not indulge with them in any sort of discussion.
Regarding the archeological evidence, there are few points that must be kept in mind. There is no way to make sure the exhaustiveness of archaeological evidence, just because some evidence hasn’t been found doesn’t mean it doesn’t exist. You cannot extrapolate the population on the basis of sample evidence found in archaeology. All such evidence stands in Isolation and it is natural and scientific to build a relationship or link of chains between civilizations but at the same time the evidence is not exhaustive and we have to way of knowing how much have we found and how much are we missing in-between that.
In order to establish Quran as a zaria-e-ilm for those who don’t believe it to be so, we first need to establish its Divine Nature through the same means of knowledge we use in every domain of life namely, observation and experimentation, induction, logical inference and established history. It is only through these means one can establish Quran as an independent source of knowledge (as done by Ghamidi Sahab in Zavia-e-Ghamidi Series).