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.
Once you have your batter, fill up the mini muffin pan as you would a regular muffin pan (filling each cup somewhere between 2/3 and 3/4 full) and pop the tray in the oven. While most cupcakes take about 15-20 minutes to bake, most mini cupcakes take from 9-14 minutes or so to reach donenss. Check your minis at 9 or 10 minutes with a toothpick and bake longer as needed.