Yeah, that would be my guess. Crystal Pepsi tastes noticeably different than regular, and caramel color is used in such small qtys that it is considered borderline flavorless.

If you look at popular grapefruit sodas Fresca is clear, but Squirt is cloudy because Fresca uses water soluble flavors and Squirt uses oils. (Squirt is the better product by far IMO because a lot of the grapefruit flavor is from the oil in the peel.)

It’s always possible the geniuses at the flavor houses Pepsi buys from have some magic I don’t know about though. But I’ve never heard of any way to make emulsified oils clear, since they refract light differently.