Lightly grease a 9-inch square metal pan, then line it with two crossed parchment strips, leaving enough overhang to lift the finished slab. Combine the fine cracker crumbs and light brown sugar in a medium bowl. Pour in the melted base butter and stir until every crumb looks evenly moistened and clumps when squeezed. Transfer the mixture to the pan and compress it firmly into a level layer with a flat-bottomed measuring cup, paying particular attention to the corners and edges.
Refrigerate the prepared base for 20 minutes while organizing the caramel ingredients. The butter needs to resolidify so the crumbs do not shift when the hot caramel is added. At the end of chilling, the surface should look matte and feel firm under light fingertip pressure, with no loose crumbs moving around the edges. Keep the lined pan in the refrigerator until the caramel is completely cooked and ready to pour.
Combine the sweetened condensed milk, dark brown sugar, caramel butter, corn syrup, and fine sea salt in a heavy 3-quart saucepan. Cook over medium-low heat, stirring continuously with a heatproof spatula and scraping the bottom and corners to prevent scorching. Once the mixture reaches a steady boil, continue cooking for 7 to 10 minutes, until it reaches 225 to 228°F. The caramel should be glossy, noticeably thick, and leave a brief trail when stirred. Remove it from the heat and carefully mix in the vanilla.
Remove the cold base from the refrigerator and immediately pour the hot caramel over it, keeping your hands clear of the steam and molten sugar. Spread the caramel into an even layer with an offset spatula, working promptly before it thickens. Let the pan stand at room temperature for 15 minutes so the strongest heat dissipates, then refrigerate uncovered for 2 hours. The center should feel cool, firm, and only slightly yielding before the chocolate layer is added.
Place the finely chopped semisweet chocolate in a dry heatproof bowl. Heat the heavy cream in a small saucepan over medium-low heat until steaming and bubbling gently around the edge, but do not boil it vigorously. Pour the cream over the chocolate and leave it undisturbed for 2 minutes. Stir slowly from the center until glossy, then mix in the softened ganache butter. Spread over the cold caramel, sprinkle with flaky salt, and refrigerate for 2 hours, until the surface is firm and no longer tacky.
Run a thin knife along any unlined edges, then use the parchment overhang to lift the chilled slab onto a cutting board. Warm a large chef’s knife under hot water, wipe it completely dry, and make four straight cuts in each direction to create 16 bars. Clean and rewarm the knife between cuts so caramel does not drag through the ganache. Let the portions stand at room temperature for 10 to 15 minutes before serving, when the caramel will be chewy and the chocolate softly creamy.