Sometimes they do contain file code numbers, or module numbers, or they look like something you've never seen before in your life. Most developers and publishers were new at this, and they didn't have any better ideas than you did on how to write the thing. In fact, I have yet to see two interactive scripts that look alike. At one of the Guild's Northern California Interactive Writers Caucus meetings, our members brought in copies of produced scripts for the sole purpose of seeing what everybody was doing in terms of formatting. We're still making it up, but we do it with a little more confidence.
Projects differ because they offer the user different types of interactivity.
Storybooks look quite different from adventure games, so it would be foolish to expect them to fit into the same format. Other times, they are very similar to feature scripts. More often than not, my final interactive scripts end up looking like a combination between a very detailed outline and a feature screenplay. Which makes sense. Being writers with a film and television background, you'd expect that we'd bring the best of our format with us.