The problem with Samuel’s prophecies is not only that they are uncomfortable, but that they come from a Lamanite. There is always a strong cultural unease with any person who is called a Lamanite. That is the point that Mormon is making. It is an interesting point, because, based on all other information we have, Samuel should not have been a Lamanite.
From Jacob’s times (see Jacob 1:13–14), the term Lamanite has been used as a collective term for not-Nephite. It functions in the Book of Mormon in the way that gentile would function for the Old Testament. When previous Lamanites have been converted, they have become Nephites. The Anti-Nephi-Lehies become the people of Ammon. The children of Amulon and his brethren, who were Lamanites due to apostasy from the Nephites and joining with the Lamanites, declared that they should be called “the children of Nephi and be numbered among those who were called Nephites” (Mosiah 25:12).
The Lamanites that Nephi, son of Helaman, converted would perhaps still be called Lamanites for either (or both) of two reasons. One is that they did not relocate and come under the Nephite government. The second is that it suits Mormon’s purposes to make certain that his readers understand that Lamanites are fully capable of true righteousness. After all, it is to future Lamanites that Mormon writes.