In both manuscripts, Oliver Cowdery initially omitted the only; and in both instances, he virtually immediately supplied the only by supralinear insertion (there is no change in the level of ink flow in either case). There would have been no motivation to consciously emend the text here by adding only since there is nothing unusual about the initially written text. Elsewhere in the manuscripts, Oliver occasionally omitted only:
In the second example, after writing “save a few guards” in 𝓞, Oliver started to write “to be led away into the wilderness”; that is, he wrote “save a few guards to”, then immediately crossed out the to and wrote inline “only to be led away into the wilderness”. And when Oliver copied the text from 𝓞 into 𝓟, he once more initially omitted the only. This time he made the correction sometime later by supralinearly inserting the only and with somewhat heavier ink flow; he probably caught this error when he proofed 𝓟 against 𝓞. But the important point of the example in Alma 58:22 is that Oliver twice omitted the only, initially in both 𝓞 and 𝓟. Thus we have firm support for the possibility of omitting only in both manuscripts for Alma 43:20.
This passage compares the battle preparations between the Nephites and the Lamanites. Both have the same kinds of weapons, but the Nephites have protective armor and clothing (as described in verses 18–19). On the other hand, the Lamanites are virtually naked. The original text uses but in this passage when making this comparison: “but they were naked save it were a skin which was girded about their loins”. In the 1920 LDS edition, this but was emended to and, undoubtedly because the only earlier in the verse already implies that they will be lacking the protective armor and clothing. Nonetheless, the use of the redundant but is intended here and will be restored in the critical text. For a nearby example of this same kind of editing of but to and in the 1920 edition, see under Alma 42:30. In both passages, the but does not reverse a previously implied negative (either another but or an only) but acts to continue the scope of the negation. In these two cases, we have a kind of multiple negation, which otherwise occurred quite frequently in the text of the Book of Mormon; for further discussion, see under negation in volume 3.
Summary: Restore the original but in Alma 43:20; even though there is a preceding only, the scope of the implied negation of the only is continued by the use of the but.