Preheat oven to 400 degrees F. Grease a muffin tin.
In a medium bowl, whisk together the all-purpose and pastry flour, baking soda, salt, and pumpkin pie spice.
In a large bowl, whisk the sugar, honey, oil and 1 egg until combined. Add the other egg and whisk well. Whisk in the pumpkin and vanilla. Whisk in the flour mixture in 2 batches, alternating with the buttermilk. Add the chocolate chips. Whisk just until combined.
Pour the batter into the prepared muffin pan. Tap the pan on the counter a few times to remove any air bubbles. Bake for 20 minutes for regular muffins (12 minutes for mini muffins) or until a wooden pick inserted in center of 1 of the muffins comes out clean. (Note: keep a close eye on these so that they do not over-bake or they tend to lose their smooth, soft texture.)
Cool on a wire rack for 15 minutes. Run a knife around the muffins to loosen them and unmold. Cool completely on the rack and serve.