Cut a slice off the stem end of each pepper, and use a sharp paring knife or pepper corer to scoop out the veins and seeds from the peppers (wear rubber gloves and avoid touching your eyes or nose).
Mix together the cream cheese, Gouda cheese, bacon bits, pineapple, and about 1 teaspoon of reserved pineapple juice, or as needed to make a workable filling, in a bowl until thoroughly blended. Using a small spoon, stuff the hollow peppers with the cheese mixture.
Place a rack or several disposable foil bread pans upside down onto a baking sheet. (See notes for how to make a pepper rack from a foil pan.) Stand the peppers, stem sides up, into the rack, and bake in the preheated oven until the peppers are softened and the filling is hot and bubbly, 30 to 45 minutes.