Gary V. Smith argues that the final line of Isaiah 6:13 (= 2 Nephi 16:13) in the Masoretic Text is original and not a later interpolation.
Gary V. Smith, Isaiah 1–39 (The New American Commentary; Nashville: B & H Publishing Group, 2007), 197–198 (Logos ed.)
6:13 The concluding verse is often read as a message of hope in the midst of destruction because it refers to a tenth being left and it mentions a holy seed. Because the Old Greek translation does not have the last line about the holy seed, because the Qumran text has a different reading, and because this phrase inserts a positive hope in the midst of a message of doom, Clements considers these hopeful ideas as late post-exilic additions to the text and not part of Isaiah’s commissioning. Making this statement more consistent with the negative tone of the passage, G. K. Beale interpreted this verse as a judgment against Judah’s idolatry because (a) elsewhere the oak tree is associated with idolatry (1:29–31), (b) the Qumran text has “high place,” and (c) maṣṣebet is viewed as a “cultic pillar” instead of a “stump.” In light of all this textual and interpretive confusion, the first thing that any interpreter must humbly confess is that the problems are numerous and difficult, without many obvious answers. Admittedly, the textual evidence of various versions points in different directions, but these changes are only a witness to the translators’ and scribes’ attempts to struggle with the obscurity of the ideas and difficulty of the theological imagery.
It is best to prefer the Masoretic reading (not Qumran or the Old Greek) and conclude that a message of hope is included, though it is a very small ray of hope. It appears that less than a tenth (presumably of people) will survive in the land, for after the forest is cut (the destruction of the land) it will be burned again (6:12–13a). This situation is compared to what happens when trees (the oak and terebinth) are cut down (6:13 b) and only a stump is left in the ground, then the remaining brush is burned. Since the holy seed comes from a stump, this must represent life that still remains in the tree that was cut down. This is mostly a discussion of hopelessness, for the positive promise is only a very small source of hope.235 The “holy seed” (zeraʿ qôdeš) is not specifically identified, but 4:3 does talk about the holy ones in Jerusalem at the end of time.
Hayes and Irvine argue that 6:12–13 uses the analogy of cutting down trees to refer to the destruction of Israel and to the fact that “the stump from which new life will grow is the house of David, the holy seed.” But similar pictures of desolation by an enemy also apply to Judah (5:29–30; 7:17–25; 8:6–9) during the coming Syro-Ephraimite War (not just Israel). The text does not refer to the stump as a “dynastic stela,” so it is impossible to identify the stump specifically with the dynasty of David. Seitz claims Isaiah refers to “graded judgments” one after the other in this passage, as in the repeated “outstretched hand” texts in 9:7–10:4, and in the historical records where Assyria gradually conquered more and more territory. First they took tribute from Israel (2 Kgs 15:29), next totally defeated Israel (2 Kgs 17), then took tribute from Judah (2 Kgs 16), and finally attacked Judah and took captives (2 Kgs 18–19). If 6:11–13a refers to that gradual and repeated process, then the stump in 13b could be the few that will be left of Judah and the holy seed might refer to the “holy ones” left in Jerusalem in 4:3. J. A. Motyer goes even further out on a limb to connect the holy seed from the stump in 6:13 to the shoot from the stump of Jesse (the Messiah) that is described in 11:1.