The theme of Bake the Cake! plays a little part as the game is mainly about putting things together. Nevertheless, some effort was put into adding ingredients and creating recipes that would make some sense and still fit into the game mechanisms.
Ingredients were chosen to fit in either only 1 part or all 3 parts. Chocolate, eggs and sugar were the ingredients I found would fit in all 3 parts.
Tools were chosen to be needed in all 3 parts. I chose 1 tool for heating (stove/oven), 1 took for cooling (fridge), 1 tool for automated work (mixer) and 1 tool for manual work (bench).
Recipes were chosen so that the parts would have a mix of ingredients used in only 1 part and ingredients used in all 3 parts. That's why there are no fruit cakes - fruits would work for toppings and fillings but not for layers.
On the other hand, it was actually the theme that brought me the idea of the final scoring: the cake contest where only the cake that most players have contributed to that counts!