init-file-user is usually rogue:
init-file-user: Hide Value Value Menu String:
State: CHANGED outside Customize; operating on it here may be unreliable.
Before worrying what to do about that, the first thing to decide is
whether this really should be defined with defcustom. I believe that
it should be defined with defvar. It seems to me that to change this
variable in a way that actually works, the user should use a command
line option such as -q or -u. Setting or saving it through Custom
appears to make little sense.
Sincerely,
Luc.