For quicker assembly, cook the tomato sauce and spelt up to two days ahead. Let cool, then store them separately in covered containers.
Pulse tomatoes with juices in a food processor until chopped. Heat 2 tablespoons oil in a saucepan over medium heat. Add onion and pepper flakes; cook, stirring occasionally, until onion is tender, about 6 minutes. Add tomatoes; bring to a boil. Reduce to a simmer; cook, stirring occasionally, until slightly thickened, about 20 minutes. Season with 3/4 teaspoon salt. Let cool.
Stir spelt into a saucepan of salted boiling water. Reduce to a steady simmer; cook, uncovered, until tender, about 40 minutes. Drain and let cool.
Meanwhile, add collard greens in batches to a pot of salted boiling water and cook until bright green and tender, about 3 minutes. Remove with tongs and let cool. Trim off stems and thick ribs. Reserve 12 large leaves; chop any remaining leaves.
Preheat oven to 375 degrees. Coarsely mash beans in a bowl. Add cooked spelt, remaining 2 tablespoons oil, cheese, sage, and any chopped collards. Stir to combine. Season with 1/2 teaspoon salt and pepper to taste.
Working with one collard leaf at a time, arrange 1/4 cup filling in center. Fold stem end over filling. Fold in sides. Roll collard over to form a bundle, overlapping ends to seal. Transfer, seam-side down, to a 9-by-13-inch baking dish.
Spread sauce evenly over stuffed collards. Cover with parchment, then foil; bake until sauce is bubbling and collards are tender, about 30 minutes. Serve immediately.