1) The file format is dependant on which app you use, or how you develop your own app. The Scanner and Room Capture sample apps from the Structure SDK export your scan by email as an OBJ file attachment. Apps from third-parties will export the file format that is preferred by that developer, but most will export the OBJ file format because this format can be imported by most 3D modeling programs and 3D printers. The Skanect Pro software for your PC or Mac computer can export your scan as an OBJ, STL, PLY, or VRML file.
If you look into the samples in the SDK, specifically the Scanner Sample App, you'll see exactly how OBJ file formats are created with the SDK. Search for email and you'll find where the code is located in the MeshViewController.mm file.
Also, you should look into the writeToFile method within the STMesh Class and the STMeshWriteOptionFileFormat Class. You can find more information on that method and all other classes within the SDK reference files.
2) The SDK was created to directly interact with the Structure Sensor and the mesh created after a scan, and not to compare multiple 3D meshes. You should look into the STMesh Class, as well.
If you'd like to do 3D mesh comparisons, you should look into Cloud Compare: