As a rule, a CTE will NEVER improve performance. A CTE is essentially a disposable view. There are no additional statistics stored, no indexes, etc. It functions as a shorthand for a subquery. In my opinion they can be EASILY overused (I see a lot of overuse in code in my job).
Check the cupcakes at the minimum baking time. If the recommended baking time is 18-22 minutes, check them at 17 or 18 minutes (just a quick peek, make sure not to let too much heat out of the oven). If the tops are rounded and no long appear wet, they may be done.
Adjust the Baking Time. If you prefer to rely on the baking temperature provided in your standard cupcake recipe, then consider lowering the baking time. If a standard cupcake takes between 20 and 25 minutes to bake, then it takes half the baking time for your miniature cupcakes. This means your cupcakes could be finished between 10 and 15 minutes. Adjust the Temperature and Baking Time