Claudio,
Partly. Of course, the inboard wing travels a bit slower than the outboard and benefits from a little more area. I tried making the outboard wing slightly large, but never managed to get the thing to turn flat. The last couple of planes I've gone to equal flap areas and it's made trimming a bit easier.
Nothing wrong with equal span wings and flaps, but I felt that the additional weight needed to keep the outboard wing from wanting to roll in was causing some problems with hinging (at least for the planes I built). It's just easier to trim the way I'm doing it now. Takes some of the elements out of the equation.