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...