Pour the coconut milk into a small saucepan and heat over low to 110°F. Place the warmed coconut milk, the ground flaxseeds, honey, and yeast in the bowl of a stand mixer fitted with the beater attachment and mix on low speed to combine. Let the mixture sit for 4-5 minutes, until it begins to foam.
Add the eggs, ghee, and vinegar to the bowl and mix on medium speed to combine. Add the arrowroot, coconut flour, baking powder, and salt, and mix again until fully incorporated. Cover the bowl with a kitchen towel and let sit for 1 hour at room temperature.
To make the everything seasoning, add all ingredients in a small bowl and stir to combine.
Preheat the oven to 350°F. Scoop the batter into a 3½-inch silicone doughnut pan, filling each cavity two-thirds full. Sprinkle the tops with seasoning and bake for 20-25 minutes, until the bagels are golden brown, and a toothpick inserted into the center comes out clean. Cool the bagels in the pan on a wire rack for 20 minutes, then remove them from the pan and cool completely on the rack.
Store in an airtight container in the refrigerator for 1 week, or in the freezer for 6 months.
*To omit the yeast, add another 1 teaspoon grain-free baking powder, and bake immediately. The texture will be a little denser and the bagels will not rise as high.