Place the flours, sugars, spices, and salt in a food processor and process briefly to combine. Add the butter and pulse 10 times, about 4 seconds for each pulse. The mixture will first look like dry sand, with large lumps of butter, then like coarse cornmeal.
Add the nuts, then process again, four or five 1-second pulses. The topping should look like slightly clumpy wet sand. Be sure not to over-mix or the mixture will become too wet.
Refrigerate the topping while preparing the fruit, at least 15 minutes.
Adjust an oven rack to the lower-middle position and heat the oven to 375 degrees.
For the filling
Toss the peaches, blueberries, zest, tapioca, juice, and sugar in a medium bowl.
Scrape the fruit mixture with a rubber spatula into an 8-inch square baking pan or 9-inch deep-dish pie plate.
To assemble and bake the crisp
Distribute the chilled topping evenly over the fruit.
Bake for 40 minutes.
Increase the oven temperature to 400 degrees and continue baking until the fruit is bubbling and the topping turns deep golden brown, about 5 minutes more.
Serve warm.
Recipe Notes
The crisp can be set aside at room temperature for a few hours and then reheated in a warm oven just before serving.