Super Rupees?

I'm not sure if it's supposed to be a mark of primitivism or of a super advanced civilization, but on Mt. Desma there's a village of rupee loving people. These people love rupees far more than those living in the town because they don't just trade rupees for useful items and information, but for every little interaction. The one beside the village entrance charges for a greeting, three vendors charge 150 rupees for relatively common items, and in the village inn there's a person who charges you to listen to him snore. Truly, this, the Yamatami tribe, is a people which loves their rupees.

Other than that, it feels like I'm just playing this game to finish it. It's not that I don't enjoy it, but there's another dungeon coming up, and outside of featuring the Tingle-slingshot minigame used to get up parts of Mt. Desma, it'll probably the same as the other dungeons. After all, each dungeon's just a means to get big rupees, and the next Super Rupee. Though, come to think of it, I'm not even sure what function the Super Rupees serve in the game.

When you throw rupees into the fountain to access new areas, you don't throw in your latest Super Rupees, just a set amount of regular rupees. They don't grant Tingle any extra abilities, and you can't sell them to get more readily usable rupees. What are they there for?

The only obvious answer is that they're Macguffins. Even then, though, just how they're arbitrary items you're collecting to move the game along is unclear. They've got to somehow relate to the final boss, but in just what way remains unclear.