The file is the document.
Most tools read a .pptx into their own model and write a brand-new file from it, so anything the model did not understand is gone when you save. PPTX Studio keeps the original package and edits parts inside it. Anything you did not touch - charts, SmartArt, animations, macros, OLE objects - is streamed back out exactly as it came in, because nothing had to understand it.