A big difference is that custom textured parts that come from the stud.io part designer have the png data contained inside the file. Standard LDraw parts use image files stored on the disk. The way these textures are referenced is also very different, so no LDraw editors or viewers display them. I'm working on adding support for embedded texture data to my blender importer that includes support for stud.io parts so that will change.
Another gotcha with stud.io is that the actual protect file itself is just a password protected zip file. This means that even if you have the password, using it is legally questionable because of laws regarding DRM.
The libraries aren't shared either, which means you'll be missing parts in stud.io that you have in regular LDraw tools, and vice versa. And stud.io parts aren't terribly well optimized.
Another gotcha with stud.io is that the actual protect file itself is just a password protected zip file. This means that even if you have the password, using it is legally questionable because of laws regarding DRM.
The libraries aren't shared either, which means you'll be missing parts in stud.io that you have in regular LDraw tools, and vice versa. And stud.io parts aren't terribly well optimized.