Is it possible to modify postgresql.conf using pg_ctl?
Reading the documentation page for pg_ctl carefully shows you what happens with the stuff you pass to it using -o:


  -o options
  
  Specifies options to be passed directly to the postgres command; multiple option invocations are appended.


So you can, for example, do the following:

pg_ctl -D {your data directory} -o "-c listen_addresses='*'" start


where the whole double-quoted expression is passed to postgres (for details, see its own documentation).

As Craig Ringer pointed out in a comment, it might be easier and, more importantly, has a lasting effect if you change these parameters using ALTER SYSTEM.