COOK pasta in a large pot of boiling water with 1 tbsp salt until tender, 11 to 12 min. Drain and set aside.
PREHEAT broiler. Cook bacon in a large pot over medium until crispy, 6 to 8 min. Using a slotted spoon, transfer to a paper-towel lined plate. Add onions and 1/8 tsp salt to same pot. Cook, stirring often, until onions are dark brown, about 12 min. Using a slotted spoon, transfer onions to a plate. Melt butter in same pot over medium-low. Whisk in flour until mixture forms a paste, about 2 min. Gradually whisk in milk. Increase heat to medium. Cook, stirring constantly and scraping the bottom of the pot, until sauce is slightly thick, 7 to 8 min. Remove from heat. Stir in gouda, 1 cup cheddar and Dijon until cheese is melted. Stir in pasta and half of bacon and onions. Scrape mixture into an 8 x 8-in. baking dish.
STIR remaining bacon and onions with 1/2 cup cheddar and panko in a small bowl. Sprinkle evenly over pasta. Broil in centre of oven until top is golden, 1 to 2 min.