Slice the caps from the tomatoes, scoop out and finely chop the pulp, and invert the hollowed shells on a rack to drain for 15 minutes; reserve the caps and pulp.
Combine the stale bread and milk in a bowl and let soak until soft, 5 minutes, then squeeze out excess liquid to make soft crumbs.
Warm the olive oil in a skillet over medium heat; cook the onion and garlic until translucent, 5–7 minutes, then stir in the reserved pulp and simmer until thick and jammy, 5–8 minutes; set aside to cool slightly.
In a large bowl, mix the ground pork, ground beef, the soaked crumbs, egg, parsley, dried thyme, the cooled pan mixture, salt, and black pepper until evenly combined without compacting.
Spoon the filling into the shells, mounding slightly, replace the caps, arrange in a snug baking dish, and bake 45–55 minutes until the shells are tender and an instant-read thermometer in the center of the filling reads 165°F/74°C and the tops are browned.
Let rest 10 minutes before serving so the juices settle.