Yes, collections can be used to filter compile, or to establish its base data source upon which further filtering is done.
For scripting, do bear in mind that with tuning the compiler can be set up to export data, rather than “documents”. You might not want or need to take it that far, into the realm of creating valid JSON or XML, but for example using a simple system of markers in a text file, like >>>> BINDER NAME to split apart outline chunks, or further break down notes and synopsis data from within those sections, would be a cakewalk for anyone that knows a scripting language.
Such a script can then be attached to your compile settings, when using TXT or Markdown-based outputs.