I opened up a .PZ3 file in a text editor, and to my surprise, some objects in my scene have extensive lines of code that seem to indicate their construction, as opposed to other props, that simply reference a file in one of my directories. Can somebody explain why this is so?

When you create a prop and add it to the library, the geometry is automatically embedded in the file. You have to manually edit the geometry out and make an external reference to an OBJ file.

Deecey's right, but don't get carried away with stripping out the OBJ just because that's the 'official' way to do things... It isn't necessarily bad to have the vertex data contained in the PZ3. When I put together a scene, I'll often make some custom props in OBJ form and put them directly in the scene, without saving as PP2. Since I always save ALL PZ3 scenes in an organized way, this doesn't clutter up Poser's libraries with little one-time-only OBJ files that would be hard to identify and way too easy to delete. It's easier to visualize and find them as part of a scene.