Melt butter in stockpot. Add shallots; cook until just starting to caramelize. Add thyme; cook 1 minute. Deglaze with vinegar.
Add Extra Melt Cheese Sauce and Cream Sauce Base; cook until melted and well combined. Add bacon, tomatoes and pasta; stir until well combined.
If desired, portion macaroni and cheese into gratin dish. Top with shredded Gouda, if desired. Broil until melted and lightly browned.