Make the Cake:
Position a rack in the center of the oven and heat the oven to 350°F. Lightly grease the sides of a 9x2-inch round cake pan and line the bottom with parchment.
Finely grate 2 oz. of the chocolate and set aside. Coarsely chop the remaining chocolate and combine with the butter and 3 Tbs. water in a heatproof bowl. Set the bowl in a skillet of barely simmering water and stir frequently until the mixture is melted and smooth. Set aside.
In a large bowl, whisk the egg yolks with 1/2 cup of the sugar and the salt until thick and lightened in color.
In a stand mixer fitted with the whisk attachment, beat the egg whites and cream of tartar at medium-high speed to soft peaks, about 2 minutes. With the motor running, gradually add the remaining 1/4 cup sugar, beating to stiff peaks, 1 to 2 minutes more.
Whisk the warm chocolate and the flour into the yolk mixture. With a rubber spatula, fold one-quarter of the whites into the chocolate batter. Scrape the remaining whites into the chocolate mixture and sprinkle the grated chocolate on top. Fold together. Pour the batter into the prepared pan and spread it evenly.
Bake until a toothpick inserted in the center of the cake comes out smudged with a few moist crumbs, about 25 minutes. Cool in the pan on a rack for 10 minutes. Run a knife around the edge of the cake and invert it onto another rack. Remove the pan and parchment and invert the cake onto the first rack (it's normal for the cake to have a crusty exterior that may crack with handling). Let cool completely.
Make the Pomegranate Jelly:
Grate enough of the apple (including the peel) to yield 3/4 cup. In a medium saucepan, bring the grated apple, pomegranate juice, sugar, and cranberries to a simmer over medium heat. Simmer, covered, until the apple is softened and the mixture has thickened a little, about 10 minutes. Uncover and continue to simmer, stirring occasionally at first and then constantly towards the end, until the liquid has evaporated and the mixture is reduced to 3/4 cup, about 5 minutes.
With a rubber spatula, press the pulp through a medium-mesh strainer into a bowl until you can't get any more juice out of the pulp. Scrape all of the juice clinging to the bottom of the strainer into the bowl and discard the pulp in the strainer.
Brush away any loose crumbs and easily detachable crusty pieces from the sides and top of the cake. Transfer the cake to a cardboard circle or tart pan bottom.
Stir the jelly to blend it, scrape it onto the cake, and spread it evenly over the top. Let the jelly cool until it's set, about 1 hour. At this point, the cake may be covered with an inverted cake pan, wrapped in plastic (the pan keeps the plastic from touching the cake), and stored at room temperature for up to 2 days.
Make the Glaze:
Put the chocolate, butter, honey, and salt in a heatproof bowl set in a skillet of barely simmering water. Stir gently until the chocolate melts and the mixture is perfectly smooth. Remove from the heat and stir in 2 Tbs. cool water. Let cool to room temperature without stirring. If not using right away, cover and store at room temperature. Set the cake on a rack set over a baking sheet. With an offset spatula, spread 1/3 cup of the glaze around the sides of the cake and on top of the gel (be careful not to disturb the gel) to smooth the surfaces and glue on any crumbs. Re-warm the remaining glaze gently to 90°F in a skillet of barely simmering water—the glaze should have the consistency of thick, pourable cream.
Scrape all of the glaze onto the top of the cake. Spread the glaze over the top and all around the sides. For the shiniest glaze, work quickly and use as few strokes as possible. Scoop up any excess glaze from the baking sheet and use it to cover bare spots.
Garnish with pomegranate seeds (if using) and let the cake rest on the rack for 10 minutes. Transfer to a cake plate and let sit at room temperature until set, 15 to 30 minutes, or up to several hours before serving.
