Line a small rimmed baking sheet with parchment paper. The toffee will not fill a full 9×13-inch pan. Have your chocolate and any toppings ready before you begin.
In a medium heavy-bottomed saucepan, combine the butter, brown sugar, granulated sugar, molasses, coffee, and salt. Cook over medium-high heat, whisking occasionally, until the mixture reaches 250°F.
Once it reaches 250°F, continue cooking, stirring constantly, until the temperature reaches 300°F, the hard-crack stage. The mixture will darken to a deep caramel color.
Immediately and carefully pour the hot toffee onto the prepared baking sheet. Quickly spread it into an even layer to your desired thickness. The toffee will begin setting quickly.
Let the toffee sit for about 1 minute. Sprinkle the chocolate evenly over the surface. Let it sit for 1 to 2 minutes, or until softened, then spread the chocolate into an even layer.
If using, sprinkle flaky sea salt over the melted chocolate.
Let the toffee cool completely at room temperature until firm. For faster cooling, you can refrigerate it.
Once completely set, break the toffee into pieces. Store in an airtight container.