The XML File stores the structure of the scene while the bin file stores large data arrays. From the XML file one can point to a byte offset of the bin file and read a number of array elements from there. For instance a mesh can have the following as normal array specification:
This line says that at byte offset 1024 a number of 100 float3 values should be read into the normal array.
For some more information look in the file app/importers/xml.cpp functions loadBinary and loadVec{2f,3f,3i}Array, etc.
