Heat the grill to medium-high.
Toss the mushrooms, oil, and a generous pinch of salt and pepper in a large bowl. Skewer the mushrooms. Cut the tops off the peppers and discard or reserve for another use. Place the peppers, cut sides down, and the mushroom skewers on the grill grate. Grill, turning the skewers occasionally, until the mushrooms and peppers have released their liquid, about 5 minutes. Transfer to dishes to cool slightly. Chop the mushrooms.
Mix the cream cheese, jalapeno, and 1 1/2 cups shredded cheese until well blended. Add the mushrooms and tomatoes and fold to mix. Season to taste with salt and pepper. Divide among the bell pepper cups. Crumble the croutons on top and sprinkle with the remaining 1/2 cup shredded cheese.
Place the pepper cups, cut sides up, on the grill, cover, and grill until the cheese melts, about 7 minutes. Serve hot.