Oliver Cowdery initially wrote natural tree at the end of the second clause in this passage, undoubtedly because natural tree had just occurred three times, so he was very much expecting it when he came to the fourth occurrence of tree. The crossout of natural appears to be virtually immediate (there is no apparent change in the level of ink flow for the crossout). Therefore, the original manuscript seems to have read “the natural branches of the tree”, not “the natural branches of the natural tree”—that is, the word natural was not repeated within this complex noun phrase.
The corrected expression “the natural branches of the tree” agrees with usage elsewhere in the text:
And there are the two examples of “the branches of the natural tree” here in Jacob 5:67–68, but there are no cases at all in which natural is repeated twice within a complex noun phrase (excluding, of course, “the natural branches of the natural tree” that Oliver Cowdery initially wrote here in Jacob 5:68).
Summary: Maintain in Jacob 5:68 the corrected reading in 𝓟, “the natural branches of the tree”.