Preheat the oven to 400ºF. Place the peppers cut side up onto the baking dish and bake for about 20 minutes.: You will notice the oven warming the kitchen and the pepper skins beginning to soften, which helps them hold their shape when filled; this brief roast concentrates the pepper sweetness and loosens the interior so the rice and filling nestle in easily. The right cue is when the edges begin to wrinkle slightly but the peppers are not collapsing, they should still feel firm when you press gently. Use a rimmed baking dish so any juices are contained. Common mistake to avoid is over roasting which makes the peppers too floppy to fill evenly, so check at 15 minutes if your peppers are small.
Meanwhile, in a heavy pan, heat the oil on medium-high heat. Add the onions and mushrooms, stir, and cook for about 7-8 minutes.: As the olive oil shimmers, the sliced onion will sizzle and begin to turn translucent, releasing a sweet aroma, while the sliced mushrooms release moisture and then brown; these changes deepen the flavor base and build the savory backbone of the filling. Keep the heat steady so the vegetables soften and pick up golden edges, stirring occasionally to promote even color. You want the onions softened and the mushrooms reduced, not steamed into limpness. One common misstep is crowding the pan which causes steaming instead of browning, so give them room or cook in batches if necessary.
Add the steak to the pan and cook for 3-5 minutes, until just done and no pink color remains. Season with salt, pepper, and red pepper flakes. Stir and remove the pan from the heat.: Once the thinly sliced beef hits the hot pan you will hear an immediate sizzle, and in minutes it will lose its pink hue and develop browned edges which concentrate savory flavor; this quick sear is key to keeping the meat tender rather than tough. Seasoning at this stage lets the flavors marry with the juices from the meat and vegetables. After tossing everything together, remove from heat to prevent overcooking while you assemble. A frequent error is overcooking the shaved steak which makes it chewy, so pull it off when just cooked through.
Place a spoonful of rice inside each pepper half (the amount of rice depends on the size of your peppers). Add a half slice of cheese on top.: The warm rice should feel slightly fluffy and will serve as a cushion that soaks up meat juices, contributing to cohesive texture. Press gently so the rice settles without compacting it into mush. Topping the rice with half a slice of cheese creates a melty layer that glues the filling together and prevents sogginess by separating rice and meat. Avoid packing too much rice which can make the center dense rather than light.
Fill each pepper with the cheesesteak mixture. Add another half slice of cheese on top of each pepper.: When you spoon in the savory mixture you should notice steamy aromas and a juicy sheen from the cooked beef and vegetables, and the filling should mound slightly without overflowing. The second half slice of cheese on top will melt into a glossy finish that binds everything when baked. Arrange the peppers snugly so they support each other on the baking dish. A common slip is overfilling which leads to spills and uneven melting, so aim for a neat mound rather than a toppled heap.
Bake for about 5-7 minutes, just until the cheese melts nicely. Garnish with freshly chopped parsley and serve.: In these final minutes the cheese will soften and become glossy, and you may hear a soft bubbling at the edges, which signals readiness; the oven also warms the filling through so flavors meld. Take care to watch closely because cheese can go from perfectly melted to browned in a blink. Once out of the oven, the chopped parsley adds a bright, fresh scent and a pop of color that makes the dish sing. Avoid leaving them in the oven too long or the cheese can develop a hard skin rather than a silky melt.