Yes, if the projected ancient samples from the Levant Neolithic are accurately placed in relationship to the modern samples, the Levant Neolithic clusters right in between the Palestinians and Jordanians to their right, and at the top left corner to the North African Jews.
The answer as to why is rather unclear to me. I think maybe the more likely scenario is that the Jews of the Bronze Age, like the Canaanites, were probably like ancient Bronze Age Levant samples, and the "Western" Jews are being pulled away by European and North African admixture. The North African ones are closer because they have less of the European gene flow. From my recollection, North African Jews are very structured by area because of endogamy as well as slightly different gene flow, but they all have a segment of ancient Jewish ancestry from colonies that existed along the coast for millennia, a Berber component of converted Jews who would have had a big chunk of Levant Neolithic, and then influx directly from Sephardim from Spain, and European Jews from Italy and other regions.
An interesting point that is once again made is the incredible variation among the "Jewish" populations. Look at the span from the Ashkenazim to the Libyan Jews, and then beyond that to the Iranian "Eastern" Jews, to the "Southern" Yemenite Jews.
Or, an alternative would be that their stay in Egypt made them different from the Canaanites, less Iranian Chalcolithic like, and they kept that difference because of all the prophets fulminating against admixture with "foreign" women.
None of this is going to be resolved without ancient samples of Jews from the Levant, imo.
Exactly what gene flow into the Ashkenazim made them so different is still a mystery to me. There they are again right next to the Sicilians, and yet IBD analysis shows no sharing between them at least from the Classical Era forward, or at least no sharing any higher than with any other group.