I've done about 50% of the classic mode and I essentially got stuck on the second one (charmeleon) for a *long* time. This led to me trying out variable strategies, especially in the third fight, where I'd get 1x, 2x, and 4x all fairly evenly. I didn't see any noticeable xp changes there.
I tested this using the same team against Youngster Joey, and I think you're right. Started with Doublade and Gogoat, the first time I won with only a Flawless Victory. I reset, picked the same team, and this time I won with both Flawless Victory and a Wipeout. And in both my exp after the battle looks exactly the same.