Preheat the oven to 425 degrees. On a large rimmed baking sheet, toss the broccolini with 1 tbsp. oil and the sliced garlic; season. Arrange the broccolini in a single layer with the garlic on top. Roast until the broccolini is crisp-tender and lightly browned, 18 to 20 minutes.
Meanwhile, bring a large pot of water to a boil for the pasta. In a large, deep skillet with a lid, heat the remaining 1 tsp. oil over medium. Add the onion; cook, stirring often, until softened, about 5 minutes. Add the chopped garlic and cook, stirring, until aromatic, about 1 minute. Add the tomatoes and the crushed red pepper; season and bring to a boil over high. Cover, reduce the heat to low and simmer until the flavors meld, about 12 minutes.
While the sauce simmers, salt the boiling water, add the penne and cook to al dente. Drain, reserving 1/2 cup of the cooking water.
Add the pasta cooking water and cheese to the tomato sauce; stir until smooth. Add the penne and stir to coat; season. Drizzle the broccolini with the vinegar. Sprinkle the pasta with the parsley and serve with the broccolini.