Thoroughly combine the meat cubes in a bowl. Cover with plastic wrap and refrigerate for at least 1 hour.
Heat your toaster oven or conventional oven to 425 ℉. Combine the onion, mushroom, bell pepper, garlic, 1/2 teaspoon of the salt, 1/4 teaspoon of the black pepper, and the olive oil in a medium bowl. Toss well then spread out on a quarter sheet pan. Roast for 30 minutes, tossing halfway through cooking, until nicely caramelized. Set aside to cool. If you are using your conventional oven, lower the heat to 325 ℉. If you are using your toaster oven, crank your conventional oven to 325 ℉.
Lube the loaf pan with nonstick cooking spray, then line it with a piece of parchment paper folded in half lengthwise to form a sling. This will aid in de-panning the loaf. Also line another quarter sheet pan with a second piece of parchment paper.
Place the ketchup, tomato paste, chipotles, adobo sauce, cocoa powder, brown sugar, and garlic powder in the bowl of a food processor. Pulse about 10 times until smooth. Transfer the glaze to a small bowl and set aside. Clean out the bowl of your processor.
Load up the processor bowl with the croutons, chili powder, thyme, remaining black pepper, and cayenne and pulse to a coarse crumb consistency, 10-12 pulses. Transfer the crumbs to a large mixing bowl.
Reload the bowl (no need to wash this time) with the roasted veggies and pulse about 5 times, keeping them on the chunky side. Add to the bowl with the breadcrumbs.
Process the meat next, in two batches until it resembles a coarse grind, 10-15 pulses. Add the meat to the breadcrumb and veggie mixture, along with the remaining salt. Mix well with your hands to combine. Beat the egg with the milk in a small bowl then add it to the meatloaf mixture, mixing with your hands again, ensuring everything is completely combined.
Place the mixture in the parchment lined loaf pan, gently pressing down to get the meat to form into the corners of the pan. Cover with the second piece of parchment and the quarter sheet pan upside down. Place one hand in the middle of the sheet pan, hold the loaf pan with your other hand and turn the whole thing over. Gently pull the ends of the parchment sling to coax the pan off the meatloaf, which should be left sitting in the middle of the sheet pan like the magnificent monument to meat that it is. Refrigerate the loaf, uncovered, for 1 hour. This is optional, but it will help to fully hydrate the breadcrumbs and allow for a better shaped loaf.
Place the meatloaf on the middle rack of the oven and bake for 15 minutes. Remove the meatloaf and brush it with about 3/4 cup of the glaze, reserving the rest for serving. Insert a digital probe thermometer in the center of the loaf at a 45 degree angle and set the alarm to 155 ℉. Slide the loaf back into the oven and continue cooking until the alarm goes off, about 45-50 minutes longer.
When finished, transfer the sheet pan to a cooling rack for 15 minutes. Then, holding one end of the parchment, slide the loaf onto a cutting board. Slice it right on the parchment using a long slicer or an electric carving knife. Do not use a serrated bread knife as it will tear the meat. If you want to slice thinly for sandwiches, allow to cool completely, then refrigerate for a couple hours before cutting.