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.
Agree with others that it really depends on your recipe and oven. I bake at just under 350 degrees F for 10-13 minutes. I always check 10 minutes in just in case. Because they're so small, it's really easy to overbake mini cupcakes and have them dry out...