I believe that the borates (which is mostly boric acid in water) and PolyQuat are compatible and do not interfere with each other. Both will inhibit, though not completely stop, algae growth. As you noted, chlorine will oxidize PolyQuat breaking it apart into smaller pieces so that creates a chlorine demand, but the smaller pieces are still effective at inhibiting algae (though they no longer act as much as a clarifier when broken up). Eventually, even the smaller pieces get oxidized, but that takes longer and is one reason why you need to add more PolyQuat weekly (in warmer water; in cooler water everything slows down).