`define-minor-mode' defines a defcustom, not a defvar, for the mode
variable. That seems like a good thing. However, if the mode has been
toggled, then `customize-customized' recognizes this variable's value as
having changed.
This can be inconvenient. Users should be able to use `customize-customized'
to check for variables that they have changed and might want to save. I use
`customize-customized' (tweaked so it always returns t) on
`kill-emacs-query-functions', for instance, to remind me to save changes. A
mode variable change via toggling is not usually a change users want to
save.