Step 1: Preheat oven to 350°F. Line a standard muffin tin with 12 paper muffin liners.
Step 2: Place almonds in a food processor; pulse until coarsely ground, about 10 times. Add flaked coconut; pulse until finely ground but still chunky, about 5 times. Transfer to a bowl; stir in oil, salt, and 2 tablespoons of the coconut sugar. Spoon 1 tablespoon mixture into each muffin liner, pressing with fingers to flatten. Bake until lightly browned and set, about 10 minutes. Remove from oven; cool 15 minutes.
Step 3: Beat Neufchâtel cheese with an electric mixer on medium speed until smooth, about 30 seconds. Add egg, yogurt, vanilla, ginger, cinnamon, nutmeg, and remaining 4 tablespoons coconut sugar; beat until smooth, about 30 seconds. Pour batter evenly over cooled mixture in muffin liners (about 3 tablespoons batter each). Bake at 350°F until centers are set but still have a slight jiggle, 12 to 13 minutes. Remove from oven; cool completely, about 30 minutes. Chill, covered, at least 1 hour or up to 4 hours.
Step 4: Stir together pomegranate juice and honey in a small saucepan; bring to a boil over medium-high. Cook, stirring occasionally, until reduced to 1/3 cup, 8 to 10 minutes. Cover and chill until ready to serve.
Step 5: To serve, remove chilled cheesecakes from muffin liners. Drizzle with chilled pomegranate syrup, and sprinkle with pomegranate seeds.