I believe I have a concise theory which explains how to trigger the glitch.
There is no negative rupee bonus with the Rupee+ skill. When you kill an enemy, there is a chance to gain a random, small amount of rupees.
Here's the thing: when killing a boss, completing a mission, or when performing a combo break or ultimate attack, the game clock pauses (not the timer, the internal logic clock) and certain game events do not fire. I assume the total pause time is baked in to the boss dying, so it triggers whether or not you do a combo break. It's just that if you don't do a combo break, you have a window to do other things, when the game isn't expecting you to.
(You can verify this when you play with two players. Have one player stand off a-ways and use an ultimate attack. Bosses' and special mobs' AI will pause until the ability is done, and enemies will not move around. The same thing happens in single player, but it makes it so much more obvious when a second player does it.)
Normally, the bonus rupees would be added to your total immediately after gaining them. But not if the game clock is paused! So this is where the glitch comes in. IF the bonus procs on the boss, and IF you get a few procs from enemies, and IF the combined total is greater than a certain number, THEN that number underflows. When the boss vanishes and the clock resumes, a negative number will be added to your rupee total.
IF that number is less than your current total, your total underflows. The game interprets this as a very large positive number. The game then caps this at 9,999,999. Tada!
The thing to test here is to play Gannondorf with Rupee+ skill and get another player to play Sheik. Without killing anything and without gaining any rupees, Gannondorf surrounds himself with a horde of weak enemies. Meanwhile Sheik goes off to the side and does the light square combo to build up special gauge. Gannondorf builds up his last combo attack (the big sweeping one) and waits. Sheik uses her special ability. During the animation, Gannondorf releases his attack. The Rupee+ bonus activates multiple times, resulting in overflow of rupee bonus, and when Sheik's animation completes (assuming the bonus comes in before the rupees gained from the enemy drops does), the total rupee count underflows and the glitch is triggered.
You're welcome, internet.