Transcripts serve two purposes - to provide additional text along with a slide, and in the case of audio presentations to present the audio in a textual format.
Usually a presentation needs to have more than just the PowerPoint slides, and the Lecturer's Notes section provides a way to include additional text along with the slide. The transcript might be the words from a lecture, or it might simply be a brief description of an image on a slide.
In the case of presentations with audio, transcripts are essential to ensure that the presentation meets accessibility requirements. Any presentation with audio is required to provide a text version of the audio that is synchronized with the presentation. In the HTML output LecShare Pro creates, the Lecturer's Notes are placed with each slide as a transcript. In the case of a QuickTime movie LecShare Pro has the option to create Quick Captions which will automatically divide up the transcript so it can be synchronized with the movie.
LecShare Pro also creates movies as SMIL files.
Read more about SMIL files.
Read more about Quick Captions