Many boxes/atoms never used?
Be careful ISO/IEC 14496 Part 10 is a video coding standard also called AVC or H.264. The associated file format is ISO/IEC 14496-15 which is based on ISO/IEC 14496-12 (aka ISOBMFF). 
A standard is the result of a compromise between different people, different companies, different application domains and different scenarios. Indeed the ISOBMFF is very wide and many boxes defined in standard may not be used in all scenarios. RTP Hint track related boxes are used only when one goal is to generate RTP packets from an MP4 file. DASH related boxes are meaningful only when you use DASH. Of course a single file may have multiple purposes and so some boxes may not be processed by some tools.