For this sentence, 𝓞 seems to have originally lacked the subject pronoun he at the beginning of the main clause (“fearing that he should not gain the point / took those of his people which would and departed”). One possibility is that Oliver Cowdery noticed the missing he when he copied the text from 𝓞 into 𝓟, with the result that virtually immediately Oliver supralinearly inserted the pronoun he in 𝓟 and at the same time supralinearly inserted the he in 𝓞. The correction in 𝓞 is with somewhat heavier ink flow, but the one in 𝓟 is without any change in ink flow.
A second possibility is that Oliver corrected 𝓞 during the dictation process. Perhaps the missing he was caught when Oliver read the text back to Joseph Smith; yet when Oliver copied this passage into 𝓟, he once more skipped the he but this time corrected the error virtually immediately.
There is clear evidence in this part of 𝓞 that Oliver Cowdery sometimes omitted the subject pronoun he as he took down Joseph Smith’s dictation. Besides the example here in Alma 46:29, there are four more in 𝓞; three of these appear to be virtually immediate corrections, without any difference in the level of ink flow (the one involving a heavier ink flow is marked with an asterisk):
There is also an instance in 𝓟, somewhat later in the text, where Oliver omitted the subject pronoun he in the main clause following a sentence-initial present participial clause:
In this instance, the 1830 edition is a firsthand copy of 𝓞, and it has the he; the correction in 𝓟 is virtually immediate, so we can be confident that in 3 Nephi 4:14 the original manuscript had the subject pronoun he.
The most reasonable assumption in Alma 46:29 is that Oliver Cowdery omitted the he, this time in both manuscripts. Even if the he in 𝓞 was supplied when Oliver copied the text into 𝓟, he was most probably correct in his assumption that the he was there in the original text.
Summary: Accept in Alma 46:29 the subject pronoun he that Oliver Cowdery supralinearly inserted in both 𝓞 and 𝓟; although his inserted he in 𝓞 may be due to conscious editing, it does appear to be necessary.