To make the dough, add whole wheat pastry flour, spelt flour, salt, and baking powder in a food processor. Pulse 2 times to combine. Pour in oil and water. Pulse until a dough forms. Remove from food processor and shape dough into a disc. Cover dough with plastic wrap and refrigerate 15 minutes.
Preheat oven to 350°F. Grease and lightly flour 6 tartlet pans.
Remove dough from oven and roll out on a floured surface. Cut out 6 circles, about 1 in larger in diameter than tart pans. Press cut out dough into prepared tartlet pans. Prick each crust a few times with a fork to allow steam to escape.
Arrange tartlets onto a baking sheet and bake for 15 minutes.
After 15 minutes, remove tartlet from oven and sprinkle crumbled goat cheese and mozzarella into each baked shell. Crack an egg into each tartlet and top with Canadian bacon, cherry tomatoes, salt, and pepper.
Bake another 10-15 minutes, depending on how runny you prefer the yolks.
Remove from oven and top with fresh thyme.