To make the butterscotch sauce. Melt the butter in a small sauce pot. Add the brown sugar, heavy cream and salt. Bring to a boil and then reduce heat to medium. Boil for 3 to 4 minutes. Remove from heat and stir in the vanilla and scotch, if using. Set a side to cool until ready to make the frosting.
Melt chocolate in the microwave on 30 second intervals, stirring between each, until smooth.
You may also use a double broiler. Dip each pretzel in chocolate, allowing excess to drip off. Place on wax paper lined cookie sheets and chill in the freezer until firm.
Preheat oven to 350 degrees F. Line a cupcake tin with liners.
Mix the canola oil and peanut butter together in the bowl of an electric mixer until smooth and creamy. Add brown sugar, sugar and eggs and beat together until fluffy. Add vanilla.
Combine dry ingredients in a bowl. Add half of the dry ingredients, mixing until just combined. Once mixed, add remaining dry ingredients. Add the milk and mix well. Fold in butterscotch chips.
Remove the chocolate covered pretzels from the freezer and place 1 or 2 in the bottom of each cupcake tin. Pour the batter into cupcake tins right over the chocolate covered pretzels and fill 2/3 of the way full. Bake for 15-20 minutes at 350. Let cool, then frost.
While the cupcakes bake, make the frosting. In the bowl of a stand mixer beat together the butter and powdered sugar until smooth and fluffy. Beat in the 1/2 cup butterscotch sauce until completely combined.
To assemble, pipe the fristing onto the cooled cupcakes. Garnish each cupcake with the chocolate covered pretzels. Then when ready to serve, generously drizzle cupcakes with the remaining butterscotch sauce. If your kitchen is hot keep the chocolate covered pretzels in the fridge until ready to eat. If you have a cool kitchen they will probably be fine on the counter.