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.
Position the oven rack to the middle position or one level below the middle. Make sure the rack is not directly on or too close to the heating element because this may burn your cupcakes. Place one or two pans in the center of the rack and add five to 10 minutes to the baking time for the silicone pan. Check that the cupcakes are cooked thoroughly by inserting a wooden toothpick into the center of a cupcake and that when removed, it slides out cleanly (i.e., no clumps or batter).