In copying from 𝓞 to 𝓟, Oliver Cowdery initially copied the hath in “after that he hath been commanded” as had. Some time later, perhaps while proofing against 𝓞 (the quill is now sharper), Oliver discovered his error and restored the original hath. The original manuscript is extant here, so there is no question that hath is correct. Probably what led Oliver to make his initial mistake is that he expected the past-tense subjunctive form had in the subordinate after-clause, especially since the preceding conditional if -clause had the subjunctive modal should. Of course, the present indicative hath can occur, but the subjunctive past-tense had is what readers expect.
Summary: The earliest text in 1 Nephi 3:18 supports the present-tense hath, not the past-tense had.