Consider the following init file:

;; Begin
(package-initialize)
(add-to-list 'package-archives
             '("melpa" . "https://melpa.org/packages/"))


(unless (package-installed-p 'use-package)
  (package-refresh-contents)
  (package-install 'use-package))


(eval-when-compile
  (require 'use-package))


(use-package slime
  :ensure t)

(setq custom-file "~/.emacs.d/custom.el")
(load custom-file 'noerror)
;; End

This will produce a following custom.el file:

(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(package-selected-packages (quote (slime use-package)))
 '(tramp-syntax (quote default) nil (tramp)))
(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 )

For some reason the tramp-syntax line gets added which causes TRAMP to load
at startup,
this didn't happen with GNU Emacs 25.3 and it slows down startup while it
gets loaded unnecessarily.
This only happens if I specify a custom-file location, if those two last
lines are deleted then
the TRAMP line doesn't get added to the init file:

;; Begin
 (package-initialize)
(add-to-list 'package-archives
             '("melpa" . "https://melpa.org/packages/"))


(unless (package-installed-p 'use-package)
  (package-refresh-contents)
  (package-install 'use-package))


(eval-when-compile
  (require 'use-package))


(use-package slime
  :ensure t)
(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(package-selected-packages (quote (slime use-package)))
 '(tramp-syntax (quote default) nil (tramp)))
(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 )
;; End

So far this happens only with SLIME and Cider packages.

In GNU Emacs 26.0.90 (build 1, i686-pc-linux-gnu, GTK+ Version 3.22.24)
 of 2017-10-13 built on lambda
Windowing system distributor 'The X.Org Foundation', version 11.0.11905000
System Description:    Debian GNU/Linux unstable (sid)

Recent messages:
Loading /home/drot/.emacs.d/custom.el (source)...
Loading tramp...done
Loading /home/drot/.emacs.d/custom.el (source)...done
For information about GNU Emacs and the GNU system, type C-h C-a.

Configured using:
 'configure 'CFLAGS=-march=native -O2 -pipe -fstack-protector-strong'
 --prefix=/home/drot/.local
 '--program-transform-name=s/^ctags$/ctags.emacs/''

Configured features:
XPM JPEG TIFF GIF PNG RSVG IMAGEMAGICK SOUND GPM DBUS GSETTINGS NOTIFY
ACL LIBSELINUX GNUTLS LIBXML2 FREETYPE M17N_FLT LIBOTF XFT ZLIB
TOOLKIT_SCROLL_BARS GTK3 X11 LIBSYSTEMD LCMS2

Important settings:
  value of $LANG: en_US.UTF-8
  locale-coding-system: utf-8-unix

Major mode: Fundamental

Minor modes in effect:
  shell-dirtrack-mode: t
  override-global-mode: t
  tooltip-mode: t
  global-eldoc-mode: t
  electric-indent-mode: t
  mouse-wheel-mode: t
  file-name-shadow-mode: t
  global-font-lock-mode: t
  auto-composition-mode: t
  auto-encryption-mode: t
  auto-compression-mode: t
  buffer-read-only: t
  line-number-mode: t
  transient-mark-mode: t

Load-path shadows:
None found.

Features:
(shadow sort mail-extr emacsbug message rmc puny dired dired-loaddefs
rfc822 mml mml-sec epa derived epg gnus-util rmail rmail-loaddefs
mm-decode mm-bodies mm-encode mail-parse rfc2231 mailabbrev gmm-utils
mailheader sendmail rfc2047 rfc2045 ietf-drums mm-util mail-prsvr
mail-utils leuven-theme time-date elec-pair tramp tramp-compat
tramp-loaddefs trampver ucs-normalize shell pcomplete parse-time
format-spec advice cus-start cus-load slime compile etags xref project
arc-mode archive-mode noutline outline pp comint ansi-color ring
hyperspec thingatpt browse-url use-package diminish bind-key easy-mmode
finder-inf info slime-autoloads package easymenu epg-config url-handlers
url-parse auth-source cl-seq eieio eieio-core cl-macs eieio-loaddefs
password-cache url-vars seq byte-opt gv bytecomp byte-compile cconv
cl-loaddefs cl-lib mule-util tooltip eldoc electric uniquify ediff-hook
vc-hooks lisp-float-type mwheel term/x-win x-win term/common-win x-dnd
tool-bar dnd fontset image regexp-opt fringe tabulated-list replace
newcomment text-mode elisp-mode lisp-mode prog-mode register page
menu-bar rfn-eshadow isearch timer select scroll-bar mouse jit-lock
font-lock syntax facemenu font-core term/tty-colors frame cl-generic
cham georgian utf-8-lang misc-lang vietnamese tibetan thai tai-viet lao
korean japanese eucjp-ms cp51932 hebrew greek romanian slovak czech
european ethiopic indian cyrillic chinese composite charscript charprop
case-table epa-hook jka-cmpr-hook help simple abbrev obarray minibuffer
cl-preloaded nadvice loaddefs button faces cus-face macroexp files
text-properties overlay sha1 md5 base64 format env code-pages mule
custom widget hashtable-print-readable backquote dbusbind inotify lcms2
dynamic-setting system-font-setting font-render-setting move-toolbar gtk
x-toolkit x multi-tty make-network-process emacs)

Memory information:
((conses 8 266033 12419)
 (symbols 24 27060 1)
 (miscs 20 115 100)
 (strings 16 51982 2324)
 (string-bytes 1 1352983)
 (vectors 8 44214)
 (vector-slots 4 834834 14348)
 (floats 8 107 14)
 (intervals 28 261 0)
 (buffers 528 12))