Here in his editing for the 1837 edition, Joseph Smith removed the first in from “commence in laboring in digging”. Probably the repetition of the in sounded strange. The removal of the first in, however, created a unique expression for the verb commence in the Book of Mormon, namely, a present participial verb form immediately following the verb commence. Elsewhere, the present participial verb form following commence is headed by the preposition in:
The example in Alma 55:25 suggests the possibility of emending in laboring in Alma 53:3 to a labor.
The original reading can, however, be maintained if one treats the second instance of “in” as an appositive to the first instance. One could show this in the standard text by placing a comma, dash, or colon between “in laboring” and “in digging”:
And as described in the following verse, the Lamanites labored not only in digging a ditch but also in building “a breastwork of timbers upon the inner bank of the ditch” and also in casting up “dirt out of the ditch against the breastwork of timbers”. In other words, Moroni’s purpose was to keep the Lamanite prisoners working, as explained in verse 5: “now Moroni was compelled to cause the Lamanites to labor because it were easy to guard them while at their labor”. Thus the original reading in Alma 53:3 is acceptable, and the critical text will restore it.
Summary: Restore in Alma 53:3 the original in that Joseph Smith deleted in his editing for the 1837 edition; some kind of punctuation break between “in laboring” and “in digging” would help show that the digging was only one aspect of the Lamanite prisoners’ labor.