Absolutely. Think of it this way, you have two ways to approach the problem:
The first is to develop a UI based on the widgets and toolkits selected by the developers. The design becomes constrained by something which has nothing to do with the way in which it is going to be used.
The second is to develop a UI based on the way in which the application needs to be used, without any artificial constraints. Sure it will be more difficult to develop, but the goal is to make a functional application, not to make it easy on the developers.