For cheese mixes, combine cottage cheese, eggs, and lemon zest in a bowl. Set aside for later. Also grate mozzarella and Provolone cheeses.
For sauce, add a drizzle of oil to a large pot or skillet over medium high heat. Add ground beef and brown well for 6-8 minutes, breaking up the beef as it browns.
Add mushrooms, onions, and garlic after beef browns. Turn heat down to medium and season with salt and pepper. Cook until veggies soften, another 6-7 minutes.
Add tomatoes to the skillet along with oregano and red pepper flakes. Bring to a simmer and turn heat down to medium-low. Let the sauce simmer for 20 minutes, stirring occasionally and breaking up tomatoes. If the sauce gets too thick, thin with a little water.
Cook ziti according to package. When ziti is boiled, drain and stir in all the meat sauce. Stir to combine.
Lay out three 8×8 freezable baking dishes. Add 1/6 of the pasta mixture to each pan. Top with 1/6 of the cottage cheese mixture in each pan and sprinkle with a tiny bit of mozzarella and Provolone. Repeat with a second layer of pasta mixture, cottage cheese mix, and more grated cheese.
If baking immediately: Cover dish with foil and bake at 350 degrees For 20 minutes. Then uncover and bake for 10-15 more minutes.
For freezing: Let dishes cool completely, then cover with a double layer of foil and freeze for up to three months.
To reheat: Move ziti straight from freeze to oven at 350 degrees F. Let bake for an hour, covered, to thaw completely and warm through. Then remove foil and let bake for an additional 15 minutes or so until ziti is bubbling in the center and warmed through.