Especially the "Merchant"-Action can be problematic:
3. Gold-Card (optional)
If you "think" an other order of cards, you may end with not as much money as intended... ^^
In my opinion playing the cards in the same order as described in the rules makes sense and is the easiest way.
There are cards that have both money and ship symbols. How should the program otherwise know which one is intended to be the "ship" card: the one with ship and 2 coins or with ship and 3 coins, just as an example.