package--ensure-init-file inserts (package-initialize) into the user's
init file, but it does not also insert (setq package-enable-at-startup nil),
which means that (according to (emacs) Package Installation) Emacs will
re-initialize the packages post-init:

 > In some circumstances, you may want to load packages explicitly in
 > your init file (usually because some other code in your init file
 > depends on a package).  In that case, your init file should call the
 > function ‘package-initialize’.  It is up to you to ensure that
 > relevant user options, such as ‘package-load-list’ (see below), are
 > set up prior to the ‘package-initialize’ call.  You should also set
 > ‘package-enable-at-startup’ to ‘nil’, to avoid loading the packages
 > again after processing the init file.