The text of the original manuscript reads as a sentence fragment: “because that part of his seed which shall be taken unto God”. The editors for the 1920 LDS edition resolved this difficulty by inserting an of after because, thereby deciding that the rest of the construction (“that part of his seed which shall be taken unto God”) was a noun phrase. For this emendation, the that acts as the determiner for the noun part.
In support of this conjecture, there is evidence in the manuscripts that Oliver Cowdery sometimes omitted the of after because (although only momentarily):
There is considerable independent evidence for the construction “that part of ” followed by a relative clause (usually headed by which):
Moreover, we have examples of “ because of that ” followed by a relative clause:
Another possibility for the sentence fragment here in the earliest text for Alma 46:25 would be to remove the relative pronoun which, giving “because that part of his seed shall be taken unto God”. In this reading, the that could be interpreted as either a subordinate conjunction or as a determiner. In the original text of the Book of Mormon (as also in the King James Bible), because that followed by a finite clause was very common. For the most part, Joseph Smith removed these instances of that after because in his editing for the 1837 edition (see the discussion under 1 Nephi 1:14 and more generally under subordinate conjunctions in volume 3).
As far as the original manuscript is concerned, it is much more likely that Oliver Cowdery accidentally omitted the of instead of accidentally inserting the which. There are a couple dozen cases where Oliver omitted the of in the manuscripts, sometimes momentarily; see, for instance, the three examples listed above where Oliver momentarily dropped the of after because. In contrast, there is at most only one example in the entire text where Oliver, depending on the analysis, may have inserted a which, namely, in 4 Nephi 1:14 (where the earliest extant text reads as a sentence fragment: “and also many of that generation which had passed away”). Yet even in that case, the larger context suggests that the which is intended (see the discussion under 4 Nephi 1:14).
Thus the most reasonable conclusion is that the 1920 LDS emendation that supplied the of is probably the original text for Alma 46:25. The critical text will accept this emendation. For an interesting case where Joseph Smith, in his editing for the 1837 edition, replaced an instance of “because of ” with a because- clause, see under Ether 1:43 (there he deleted the of and the relative pronoun which).
Summary: Accept in Alma 46:25 the 1920 LDS emendation with its added of in “because of that part of his seed which shall be taken unto God”; scribal errors and usage elsewhere in the text strongly support this emendation.