The Nephites understood that God was Jehovah, and that Jehovah would come to earth as the Messiah. Thus, when Nephi says that “even the very God of Israel do men trample under their feet,” he means Jehovah in his earthly mission.
It is that connection to the earthly mission of the Messiah that leads directly to the six hundred-year prophecy—that the Messiah would come six hundred years after Lehi left Jerusalem. Even after the first discussion of the small plates in 1 Nephi 9, Nephi followed that information with a discussion of the earthly mission of the Messiah, including the six hundred-year prophecy (1 Nephi 10:4).
This is an important prophecy, but a difficult one for modern readers. The best scholarly estimates for the year of Jesus’s birth is 6–4 B.C. The departure from Jerusalem was perhaps in 597 B.C. That does not allow for six hundred years, yet the Book of Mormon counts them down to the year. The logical solution to this is that the Nephites followed a different year. In the Old World, Israel used a lunar year of about 357 days rather than a solar year of 365 days. This later changed to the solar year, although the community of Qumran felt that the lunar year should still be the standard. In the New World, Mesoamerican peoples had multiple calendars, but one was based on a 360-day year. Using either of those shorter years, the fewer days added up to sufficiently fewer solar years that there were just the six hundred years according to the lunar calendar, or a little longer if using the 360-day year. The difference between the two falls into the 6–4 B.C. range for the birth of Christ.