Set the oven to 350°F, then cook the shells in a large pot of boiling salted water for 1 minute less than the package’s baked-shell directions; scoop out 1 cup of cooking water before draining and rinsing the pasta under cool water. The cooled shells should bend without collapsing, making them easier to fill.

Warm the olive oil in a large skillet over medium-high heat, soften the onion for 3 to 4 minutes, then break the beef into crumbles with a wooden spoon and cook for 5 to 7 minutes before draining excess grease. Look for softened onion and browned, fully cooked meat rather than wet clumps.

Stir the tomato paste, chili powder, cumin, paprika, crushed red pepper flakes, garlic powder, black pepper, and 1 teaspoon salt into the beef for 1 to 2 minutes, then mix in 1/2 cup salsa and the reserved cooking water and simmer on low for about 2 minutes. The spices should smell fragrant before the liquid goes in, and the mixture should thicken slightly during the simmer.

Blend the cream cheese into the filling over low heat until no visible cubes remain, then take the skillet off the burner and allow 5 to 7 minutes of cooling. The mixture should look creamy and hold together on a spoon rather than separate into meat and liquid.

Coat the bottom of the 9-by-13-inch dish with the remaining salsa, spoon the beef filling into the shells, and place them opening-side up before scattering the shredded cheese over them. Keep the shells supported by their curved bottoms so the filling stays inside.

Bake for 20 to 25 minutes, checking for bubbling salsa and a golden cheese topping. The cheese should melt across the shells, with bubbling around the edges signaling that the casserole is hot.