Date: Thu, 19 Nov 2015 13:27:29 +0100
From: Andreas Röhler<andreas.roehler@easy-emacs.de>
A way around is to start with -Q and load init-file interactively.
However then saving options via customize isn't possible, which seems a bug.
No, it's a deliberate feature. From the Emacs manual:
If Emacs was invoked with the `-q' or `--no-init-file' options
(*note Initial Options::), it will not let you save your customizations
in your initialization file. This is because saving customizations
from such a session would wipe out all the other customizations you
might have on your initialization file.