Not sure if this helps, but Rapid Shot clearly states that it allows for one extra attack per round with a ranged weapon.
In the equipment chapter, it clearly states that ranged weapons are thrown weapons or projectile weapons that are not effective in melee.
Also in the equipment chapter, under Crossbow, Heavy it states that "The Two-Weapon Fighting feat does not reduce these penalties because it represents skill with melee weapons, not ranged weapons.
With the Shuriken, it seems that as written Rapid Shot and not TWF would apply. With Crossbows, the argument could me made I suppose that the writers simply meant the reduction in attack penalties, but to me it looks like they meant the feat in general didn't work for ranged weapons.
My conclusion is that you can only use the quickdraw/rapid-shot combination if you are using weapons that you can not use effectively in melee (darts, javelins, shuriken, etc) and that you can only use the quickdraw/TWF throwing combination if you are using melee weapons with a range increment.
Flurry is a special case, however I think the rule still applies in regards to throwing. You obviously can Flurry with Shuriken, but you have to apply Rapid Shot and not TWF for additional attacks per round. If you used Sai, you would apply TWF and not Rapid Shot as Sai is a Melee weapon (which has a range increment).
Just my 2 cents.