I have done that type of hinging before but decided to fallow the building instructions as much as possible this time, I think the hinging the designer recommends works just fine and thats why I will go with the way he has design it.
The thing with us ( kit builders ) is that we can easily replace a step with what we think is acceptable for us and that's the beauty of building an airplane made out of balsa and ply.

I too thought of hinging the flap hinges on an angle but ( for me ) I don't see the need to modified that step at this time.

If you decide to hinge the flap with the hinges on an angle I like to suggest you make yourself an angle tool made out of ply and a small piece of brass tube to guide the drill at the same angle on every hole you will be making.