Royal Supplier in Puerto Rico Expansion II -- is it all or nothing?
I can find no ruling on this, but there's some precedent to work with.

In the first expansion, the Small Wharf:


  A player may ship different barrels of
  goods during one of his turns during
  the captain phase, but he gets only 1
  VP for every two barrels he ships.


Further clarifications on that building show that a player can ship &lt; 2 goods*, and need not ship all remaining goods.

So, I'd reason based on precedent (and in the absence of any other errata) that buildings that modify the captain phase allow the player to choose the selection of goods involved.

Thus,

Scenario 1: You can send up to 5 goods (1 of each kind) to the royal treasury.

Scenario 2: Likewise, you may send up to 2 goods, provided they are different, to the royal treasury.

*There's some deviousness to be had in combination with Lighthouse, and effectively trading for 1 doubloon at the end of every Captain.