Heat olive oil in large skillet over medium-low using measuring cup. Add sliced onions and garlic with wooden spoon. Cook 25-30 minutes stirring often till deep golden jammy soft, no burn.
Stir crushed tomatoes, red pepper flakes, salt, pepper from measuring spoons into onions. Simmer 10 minutes thick glossy with wooden spoon. Taste adjust salt.
Boil large pot salted water. Add rigatoni, cook al dente per box minus 1 minute. Reserve 1 cup pasta water with measuring cup. Drain colander.
Add pasta to skillet sauce with tongs. Pour ½ cup reserved water. Toss vigorous wooden spoon 2 minutes till sauce clings glossy. Stir parmesan till melted creamy.
Plate pasta twirls. Tear basil over top. Grate extra parmesan. Hit table steaming.