I make Biscotti on a regular basis and from the recipe you used, I can see a few thing that might help.
The recipe has you jumping through unnecessary hoops.
Pulse the almonds in the first part and set aside. ground the almonds from the second part, place them in the bowl with all the dry ingredients, then add the wet (eggs, vanilla, etc...) and mix until just combined.
The baking powder is not enough in the recipe to raise the dough....I can see that clearly.
For 2 cups of flour I use 3 eggs and no whites.
2 teaspoons of salt? wow......
No wonder they came out flat.
2 1/2 cups flour
3/4 cup sugar
1 teaspoon Baking powder
1/4 teaspoon salt
1 teaspoon vanilla extract
1/2 teaspoon almond extract
1 cups chopped almonds.
Mix dry ingredients add wet, stir to just combine. Shape into loaves bake 350 for 8 minutes, turn pan, bake 10 minutes mores Remove and slice then rebake for 10 minutes again, turn pan and finish to desired dryness.