postgresql.conf file found in both /usr/share/postgresql and /etc/postgresql/
Files below /usr/share/postgresql/ are supposed to be data files that are not meant to be edited. They are not live configuration files.
The FHS spec at https://wiki.debian.org/FilesystemHierarchyStandard
defines /usr as:

/usr/
Secondary hierarchy for shareable, read-only data (formerly from UNIX source repository, now from UNIX system resources)
(files that are not-required to boot or rescue the system)

[...]
/usr/share/ : Architecture-independent (shared) data
[...]

On the other hand, files under /etc/postgresql/X.Y/main are the live configuration files for a PostgreSQL cluster named main with version X.Y, such as created by the command pg_createcluster. Each cluster (=each postgres instance) has its own postgresql.conf that is generated with it, as the other writable configuration and data files of that cluster.
Personally, on my Ubuntu 14.04, I don't find a postgresql.conf under /usr.
There is however a template file at /usr/share/postgresql/9.3/postgresql.conf.sample, but note the .sample suffix.
That file belongs to the postgresql-9.3 package, as revealed by dpkg -S:
$ dpkg -S /usr/share/postgresql/9.3/postgresql.conf.sample
postgresql-9.3: /usr/share/postgresql/9.3/postgresql.conf.sample

It's also consistent with
http://packages.ubuntu.com/trusty/amd64/postgresql-9.3/filelist
You may try dpkg -S postgresql.conf on your system and check if /usr/share/postgresql/9.3/postgresql.conf is part of the results, and if yes, to what package it belongs, and then what is the origin of that package. Maybe for some reason it's the same as the sample postgresql.conf, except it doesn't have the .sample suffix.