Idem significat utrum "quod" pronomen, ut puto, Rufe Rutile. Magis autem primum pronomen, secundum conjunctio. Non mala est latinitas, nisi fallor, at non classica:
Both the same, I think, at least in English, "that". No, rather the first is a pronoun, the second is a "conjunction". I think the Latin is OK, though not classical:
"On the refutation of that which they say, that glorious God may be at a distance, that he ignores particulars..."
I'm writing in Latin hoping for correction, and not because I'm confident in how I express myself. Latinè scribo ut ab omnibus corrigar, non quod confidenter me exprimam.