To prepare dough, dissolve honey and yeast in 1 cup warm water in a large bowl; let stand 5 minutes. Lightly spoon flours into dry measuring cups; level with a knife. Add 1 1/4 cups all-purpose flour, whole wheat flour, salt, and 1/8 teaspoon freshly ground pepper to yeast mixture; stir until a soft dough forms.
Turn dough out onto a lightly floured surface. Knead until soft and elastic (about 6 minutes); add enough of remaining all-purpose flour, 1 tablespoon at a time, to keep dough from sticking to hands (dough will feel slightly sticky). Knead in fresh basil just until incorporated. Place dough in a large bowl coated with cooking spray, turning to coat top. Cover and let rise in a warm place (85°), free from drafts, 40 minutes or until doubled in size. (Gently press two fingers into dough. If indentation remains, dough has risen enough.)
Roll dough into a 12-inch circle (about 1/4 inch thick) on a lightly floured surface. Place dough on a rimless baking sheet sprinkled with cornmeal. Crimp edges of dough with fingers to form a rim. Lightly spray surface of dough with cooking spray; cover with plastic wrap. Place dough in refrigerator.
Position one oven rack in the middle setting. Position another rack in the lowest setting, and place a rimless baking sheet on the bottom rack. Preheat oven to 500°.
Remove plastic wrap from dough; discard. Remove preheated baking sheet from oven; close oven door. Slide dough onto preheated baking sheet, using a spatula as a guide. Bake on lowest oven rack at 500° for 8 minutes.
Arrange tomato slices on paper towels. Cover with additional paper towels; let stand 5 minutes.
Sprinkle fontina over crust, leaving a 1/4-inch border. Arrange tomato slices and olives over fontina; sprinkle with mozzarella. Top with pine nuts. Bake on middle rack an additional 8 minutes or until crust is golden brown and cheese melts. Garnish with cracked pepper, if desired. Cut into 12 wedges.