Preheat oven to 400°F. Combine soy sauce, molasses, ginger, vinegar, and garlic in a small saucepan over medium. Cook, stirring often, until mixture simmers and reduces to about 1⁄2 cup, about 2 minutes. Remove from heat.

Thinly slice green parts of scallions; reserve. Cut white parts of scallions into 1-inch pieces, and place on a large rimmed baking sheet. Add sugar snap peas and bell peppers. Drizzle vegetables with oil, and toss to coat. Spread in an even layer.

Place salmon fillets, skin side down, nestled in vegetable mixture; spoon about 1 tablespoon molasses mixture over each fillet. Reserve remaining molasses mixture. Sprinkle salmon and vegetables evenly with salt and pepper. Place in preheated oven, and bake until vegetables are tender and lightly browned, salmon is cooked to medium, and glaze is golden, 16 to 18 minutes.

Prepare rice according to package directions; divide evenly among serving plates. Place salmon and vegetables on plates; sprinkle with scallion slices and sesame seeds. Serve with remaining molasses mixture and, if desired, lime wedges.