My guess is that limonin is responsible for the orange juice in the glass bottles not tasting as good as the carton juice. Limonin is a very bitter substance naturally arising from orange juice. Removing it is difficult and limited by patents. The Tropicana's of this world (which tend to sell in cartons) use centrifuges and these special beads to debitter the juice, but other companies resort to mixtures of Valencia juice (which doesn't produce juice that goes bitter after a few hours) with other less expensive cultivars that will add bitter notes.
The limonin develops a few hours after the juice is squeezed. So if the juice is fresh, it is the balance of sugar and acid in the fruit that has the biggest impact on its flavor. Also, commercial juice needs to be pasteurized, which add to the flattening of the flavor.
The soda-lime glass used for containers in the US and many other countries leach very little of their elements into a solution as acid as orange juice (recycled glass leaches more and glass with phosphates, less).