Make the cupcakes: Preheat the oven to 350 degrees F. Line a 6-cup muffin pan with paper liners. Whisk the cocoa powder with 1/3 cup hot water in a bowl. Whisk in the chocolate syrup until smooth; let cool slightly. In a large bowl, whisk the flour, granulated sugar, baking soda, baking powder and salt.
Whisk the vegetable oil, egg, milk and vanilla into the cocoa mixture until smooth, then fold into the flour mixture until just combined. Divide among the muffin cups. Bake until a toothpick comes out clean, 18 to 20 minutes. Let cool 10 minutes in the pan, then remove to a rack to cool completely.
Make the frosting: Put the chocolate in a microwave-safe bowl; microwave on 70 percent power in 30-second intervals, stirring, until melted. Let cool slightly. Beat the butter, vanilla and confectioners' sugar with a mixer on medium-high speed until fluffy. Add 3 tablespoons milk; beat until smooth, 3 minutes. Remove half of the frosting to a separate bowl; add the cocoa powder, melted chocolate and a pinch of salt and beat until fluffy, 2 minutes. Mix the remaining 1 tablespoon milk and the malted milk powder in a cup, then add to the plain frosting; add a pinch of salt and beat until fluffy, about 2 minutes. If the frosting is too soft, cover and chill until it is firm enough to pipe.
Frost the cupcakes (see below) and top with pretzel rods.
How to swirl the frosting:
Put the 2 frostings in separate pastry bags (or zip-top bags). Snip off the tips. Position side by side in another pastry bag fitted with a large star tip.
Pipe the frosting onto the cupcakes in a spiral motion to create a swirl.