I'm running my own emacs config that resides in non-default place. So I use -Q -l startup options. I've defined place for saving customization and set custom-file variable accordingly.
Unfortunately emacs refuses to save my custom options motivating it with possible harm to original options. But I know what I do, and I what to have separate custom file filled with current session variables?
How can I overcome emacs restrictions?
emacs manual says:
If Emacs was invoked with the -q or --no-init-file options (see 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.