[The] init file [...] specifies how to initialize Emacs for you.
[Therefore it is normally located in (a subdir of) your home directory.]
[You] may also have a site startup file [...] named
site-start.el. [It is normally located] in a subdirectory named
site-lisp in the Emacs installation directory, such as
/usr/local/share/emacs/site-lisp [but] you can place [...]
site-start.el in any of the directories which Emacs searches for Lisp libraries.
We recommend against using
site-start.el for changes that some users may not like.
(see The Emacs Initialization File)
In a multi-user environment, as an admin, you put in
site-start.el the customisations intended for all users, while single users will use their own init file.
Also, if you make a customised Emacs distro, you put specific distro packages, together with
site-start.el, in the
Before the personal computing era, having a centralised Emacs server was a necessity due to the mainframe computing model, which required so called site customisations. A typical scenario nowadays is that each user has their own Emacs on their own computer, perhaps a laptop. Therefore there is not much need for site customisations, including
Anyway you might use Emacs as a daemon to manage your emails, you org agenda notifications, etc. In this case
site-start.el is the proper place to craft your daemon.