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.
If you only have one muffin pan and a recipe calls for more cupcakes than your pan will make, cover and refrigerate the rest of the batter while baking the first batch. Cool the pan for 15 minutes after it comes out of the oven and then bake the rest of the batter adding one to two minutes to the bake time.