I remember Konami had an Ultra label before to circumvent the publishing limitations set by Nintendo. TNMT and Snake's Revenge (a non-canon Metal Gear) was released on that label.
There's no reason to release a game with a different label, unless they don't want the game to be associated with the main brand. Maybe Namco wanted to be experimental with some game ideas, and don't want it to be attached with that brand in case it flopped.







