It wouldn't make sense for the engine to compress / convert / include what isn't directly linked to the ved itself. It'd probably have a field day if it tried to include every file found in each sub folder seeing as there's probably various file types in said folders that aren't supported by VS (psd & video project files maybe & so on).
RPG Maker includes every files when builds. Furthermore, newest version, RPG Maker MV, puts unnecessary RTP so every game built by this engine has at least more than 400MB no matter original files included or not.
Well. I wonder other game engines handle just like VS. Curious.