You'll have to do things manually. You can create prizes for each item and select "Manual" for the "Recipient". You'll have to award them by selecting the recipient (once known) in the "Override" section.
For the "royal flush" prize, I would create a 2nd rake as you described. If someone gets a royal flush during a tournament, (a) add any money from previous tournaments to the pot by using the "House Contribution" field on the Game tab; (b) create another manual prize; (c) award the prize using the override section.
All manual and a little bit tedious, but there's really no way for the software to know enough to do this automatically anyway. By going through all of these steps, the stats will be aware of the prizes won by these players.