The only "cure" for this is to use the new approach introduced with GNU Emacs 25.1:
--8<---------------cut here---------------start------
------->8---
(package-initialize)
(add-to-list 'package-archives
'("melpa" . "https://melpa.org/packages/"))
(setq package-selected-packages '(slime))
(unless package-archive-contents
(package-refresh-contents))
(package-install-selected-packages)
(setq custom-file (locate-user-emacs-file "custom.el"))
(load custom-file 'noerror)
--8<---------------cut here---------------end--------------->8---
This will avoid writing the custom.el file with the "package-selected-packages" variable since it's already there
and no TRAMP variable will be added to the custom.el file.
So in short, it seems that the "tramp-syntax" variable gets caught along with "package-selected-packages"
and it gets written to the custom file whenever we use "package-install" or "use-package" (which also uses "package-install")
instead of "package-install-selected-packages".
This didn't happen wtih GNU Emacs 25.3, why it happens now I don't know.
Thank you again,
Davor Rotim