Why is the System tablespace in manual segment space management mode?
Because Oracle says so :). The official documentation explicitly states that:


  Restrictions on Automatic Segment-Space Management This clause is
  subject to the following restrictions:
  
  
  You can specify this clause only for a permanent, locally managed tablespace.
  You cannot specify this clause for the SYSTEM tablespace.
  


I don't know why, there are some hypothesis here.