The two do NOT belong together - UNLESS the abandoned fan-fic FAMILY is taken into consideration. There the Disney toons and the Warner toons work in neighboring studios, and Disney generally worked with less endowed toons (hammerspace, etc. are the powers of Warner toons). The chapter where Wakko and 3 Tiny Toons invade the Disney soundstages to have it out with Darkwing is about the most hilarious yet !
It's NOT a film, it's a fan-fic and you'll find it on the fan-fic.com website, Under Cartoons/Animaniacs. The title is "FAMILY" and it's all how the Warner kids got into show-biz -it dismisses the water-tower years as studio hype. BUT There IS friction bet Yakko and Plotz.
Speed up searching by clicking on "drama". The story tends to be episodal, but pics depicting the action at points can be found here under "Warners", esp. the one with Darkwing snarling at the Warners who are taunting him. This clash leads to the Warner-Disney WAR that so hilariously follows.