In a medium saucepan, combine the stock and 1 cup of water and bring to a boil. Keep warm over very low heat.

In a large saucepan, heat 1/4 cup of oil. Add the shallot and cook over moderate heat, stirring, until softened, about 3 minutes. Add the penne and stir constantly for 2 minutes. Add the wine and simmer, stirring, until absorbed, about 2 minutes. Add 11/2 cups of the warm stock mixture and cook over moderate heat, stirring, until nearly absorbed. Stir in the marinara sauce; bring to a simmer. Continue adding the stock 1/2 cup at a time, stirring frequently, until nearly absorbed before adding more. The pasta is done when its al dente and the sauce is thick, about 25 minutes total.

Meanwhile, in a skillet, heat the remaining 1/4 cup of oil. Add the garlic and cook over moderately high heat, stirring, until fragrant but not browned, about 2 minutes. Add the tomatoes and a generous pinch each of salt and pepper and cook, stirring, until just starting to soften, 3 to 5 minutes.

Add the tomatoes to the pasta and cook over moderate heat, stirring, for 2 minutes. Stir in the 3/4 cup of basil and season with salt and pepper. Transfer the pasta to bowls and garnish with the zucchini blossoms (if using) and basil. Serve right away with cheese.