Here the 1837 edition inserted the perfective had in the when-clause. This addition was probably unintentional since elsewhere in the text there are six other examples of “now when X (had) heard these words” yet none of these have ever had the perfective had added or deleted. Four of the six other instances have the had, but two lack it:
So the best solution is to accept in each case the earliest extant reading, which means that here in Alma 20:16 there is no perfect auxiliary in “now when his father heard these words”.
Summary: Restore the earliest reading for Alma 20:16, the one without the perfective had (“now when his father heard these words”).