Here the earliest text reads “the Son of the Only Begotten of the Father”. The extra of after Son appears to be an early error in the transmission of the text (either when the scribe in 𝓞 took down Joseph Smith’s dictation or when scribe 2 of 𝓟 copied the text from 𝓞). The same error appears later on in the book of Alma:
In both cases, scribe 2 of 𝓟 was the one who copied the text from 𝓞 into 𝓟. Joseph Smith, in his editing for the 1837 edition, deleted the extra of in both these passages. Literally, the earliest text for these two passages says that there is a son of the Son of the Father, which contradicts all other uses in the Book of Mormon of the phrases “Only Begotten Son” and “Only Begotten of the Father”. Otherwise, these phrases always refer to the Son of God, not to a son of the Son of God:
The error “the Son of the Only Begotten of the Father” in Alma 5:48 and Alma 13:9 appears to be a blend of the very frequent “the Son of God” with “the Only Begotten of the Father”. Elsewhere in the original text, the phrase the son is modified by an of-initial prepositional phrase 131 times, while the son alone (without any following of-phrase or any other kind of postmodification, such as a noun phrase in apposition) occurs 23 times. Thus there is a rather high expectation that there should be an of between the son and an immediately following noun phrase. In other words, the correct appositive usage in “the Son / the Only Begotten of the Father” would have been highly unexpected, thus leading to the accidental intrusion of an extra of in both Alma 5:48 and Alma 13:9.
David Calabro (personal communication) suggests another possible emendation for Alma 5:48 and Alma 13:9: namely, the original text may have read “the Son of God / the Only Begotten of the Father”, which would mean that for this expression the word God was twice omitted during the early transmission of the text. Indeed, there is evidence elsewhere that the scribes occasionally omitted God:
But the loss of God in all these examples is only momentary. In my mind, it is much more probable that the function word of was accidentally inserted twice in the unusual expression “the Son / the Only Begotten of the Father” than the noun God was accidentally deleted twice from what sounds perfectly normal, “the Son of God / the Only Begotten of the Father”.
Another possibility, also suggested by David Calabro (personal communication), would be to maintain the of in both these passages but to punctuate it so that it could be interpreted appropriately. For instance, one could interpret “the Only Begotten of ” as a rephrasing of “the Son of ”:
In other words, this complex noun phrase would be equivalent to “the Son of the Father / the Only Begotten of the Father”, with ellipsis in the actual text of the first the Father. Another possibility, applicable only to the second case (Alma 13:9), would involve the noun order:
Here the equivalent reading would be “the order of the Son / the order of the Only Begotten of the Father”, with ellipsis in the actual text of the second the order. Of course, this second interpretation cannot apply to the first case (Alma 5:48) since the noun order is not there. But more significantly, there is no evidence elsewhere in the Book of Mormon text for complex chains of prepositional phrases with these kinds of ellipsis. The easier solution is to simply assume that the extra of in “the Son of the Only Begotten of the Father” is intrusive.
Summary: Accept in Alma 5:48 and Alma 13:9 Joseph Smith’s emendation of “the Son of the Only Begotten of the Father” to “the Son / the Only Begotten of the Father”; the extra of seems to have been the result of expecting of after the son when immediately followed by a noun phrase.