Place muffin liners in two 12 cup muffin tins. Preheat oven to 350 degrees Fahrenheit.
Combine flour, salt, baking soda, baking powder, cinnamon, and pumpkin pie spice in a medium bowl and stir with a whisk.
Combine water and flaxseed in a small bowl and set aside.
Combine sugar, canola oil, honey beer, egg substitute, and eggs in a large bowl and beat with a mixer at medium-high speed until well blended.
Add the flaxseed mixture and pumpkin and beat on low speed until just blended.
Add the flour mixture and beat until combined.
Fold in the chocolate chips, reserving 1/3 for later.
Fill each muffin liner with 1/4 cup batter. Sprinkle each muffin with the remaining chocolate chips.
Bake for 20 to 25 minutes or until a toothpick inserted comes out clean.
Let cool for 10 minutes in the pan before taking out and cooling on a wire rack.