Heat olive oil in a large skillet over medium-low heat. Add shallots and cook, stirring occasionally, until the shallots have become totally softened and caramelized with golden-brown fried edges, around 20 minutes. Add Swiss chard and garlic, and sauté for 5 more minutes.
Add red-pepper flakes and miso paste. Stir to combine, and cook about 2 minutes.
Add tomato paste and black pepper. Cook, stirring frequently, until the tomato paste has started to cook in the oil a bit, deepening in color, about 2 minutes. Remove from heat and transfer about half the mixture to a resealable container (I recommend placing this in the freezer after it has completely cooled).
To serve, cook pasta according to package instructions in a large pot of salted boiling water until very al dente. Transfer to skillet with remaining shallot mixture and 1 cup pasta water.
Cook over medium heat, using tongs to turn and coat pasta, using a wooden spoon or spatula to scrape up any bits on the bottom, until pasta is thick and sauce has reduced, 3 to 5 minutes.
Serve pasta garnished with parsley and flaky sea salt.