Bring a large pot of salted water to a rolling boil for the pasta.
In a large non-stick skillet over medium heat, warm the olive oil, then add the crushed garlic and crushed red pepper flakes; cook, stirring, until the garlic is fragrant and just begins to brown, about 2–3 minutes.
Add the chopped canned whole peeled tomatoes to the skillet and simmer over medium-low heat for about 10 minutes to reduce and meld flavors.
Add the fresh cherry tomatoes to the sauce and simmer for another 10 minutes until they begin to soften.
Stir in the drained cannellini beans and return the sauce to a gentle simmer; season with sea salt to taste and keep warm over low heat.
Cook the whole grain penne in the boiling water according to package directions until al dente, taking care not to overcook.
Drain the pasta well and transfer it to a large bowl.
Add the hot tomato and bean sauce and the baby arugula to the pasta and toss with a large spoon until the arugula wilts and everything is evenly combined.
Divide pasta among warm bowls and top with good quality grated Parmesan if desired.