The problem with building a mock-up in Supercard or Director is that turning such a prototype into a shippable program requires a complete re-implementation of the program in a new tool (probably INDIE). Supercard and Director use languages and representations that are largely scripting tools. To support INDIE questions, one needs answers, rules, widgets, and screens, complete with hyperlinked data, nested structures, and modern model/interface separation. This is well beyond the scope of a scripting language. So, after spending time and effort building such a mock-up, helpful as it was in the early stages, authors would get little or no reuse of this artifact in the final product outside of a few bits of art and video.
The major issue for product delivery is to consider the total length of time on the project. If the project is completely re-implemented in a new tool, a very large portion of the time spent building the mock-up will be wasted, thus increasing the total project length. If authors started building on the final delivery platform from the beginning, the time spent on walkthroughs isn't wasted; the walkthrough becomes the basis for the shippable application. However, authors couldn't afford to spend the time up front due to short deadlines at the beginning of the project.
Even worse from the perspective of final delivery, authors are likely to (and did) design interface and model interactions that are difficult or impossible to implement for real as they felt no restrictions from their mock-up tool. Authors, especially non-programmers, who aren't familiar with INDIE's strengths and limits as well as the limits of what any program can be made to do in a reasonable amount of time, will construct almost anything.
It was clear that we needed to get the authoring of storyboard-level interfaces into the hands of authors and out of the hands of programmers. At the same time, we had to preserve the the model that the full-scale application would require.