The bothersome phrases are: non est hoc quod ipsa . . . [and] non erat quod ipse.Nec mouere debet, quod, cum sit inuisibilis, saepe uisibiliter patribus apparuisse memoratur. Sicut enim sonus, quo auditur sententia in silentio intellegentiae constituta, non est hoc quod ipsa: ita et species, qua uisus est Deus in natura inuisibili constitutus, non erat quod ipse.
Translation: Neither should it bother us that God, although he is invisible, is described [in the Bible] as appearing visibly to the [Old Testament] patriarchs. Just as a sound, by means of which a thought is established in the silence of the mind is not the same thing as the thought, so also God, in his nature invisible, is not the same as the appearance that is seen by men.
In both troublesome phrases, I read quod as a relative pronoun and supply a form of sum. Like this:
non est hoc [antecedent is sonus] quod ipsa [antecedent is sententia] est
non erat [subject: Deus] quod ipsa [antecedent is species ] erat