Preheat oven to 425F. Line two baking sheets with parchment paper. Set aside.
In a large bowl, combine flour, baking powder, baking soda, salt, and sugar. Cut in coconut oil until crumbly. Mix in yogurt, eggs, cream, and vanilla until a shaggy dough forms. Mix in apples and pecans.
Turn dough onto a floured surface and gently knead several times until dough comes together. Divide dough in half and pat each half into a 1-in thick round. Cut each round into 8 wedges and place wedges on prepared baking sheets.
Bake scones at 425F 13-15 minutes or until golden-brown. Remove from oven and cool on a wire cooling rack.
Make the caramel glaze: In a small saucepan, bring butter, sugar, and agave to a low boil, stirring occasionally until golden-brown and caramel is slightly thickened. Remove from heat and whisk in baking soda and salt.
Drizzle warm caramel glaze over scones and serve. Enjoy!