Master tonberries are found about 23.76% more often in the areas illuminated by the Purple crystal things. This has been proven on 29 different save files out of 32.
As for Tonberries The area where the right turns into a large room in the sunken cave has a higher percentage chance for them there. Magic Pots are found less because their percentage 29.46% is reduced and Tonberry is increased. I'm not sure about how much Magic Pot is Reduced but there is Definently a Distinct difference about tonberry encounters there.