Toggling a mode changes the value of the mode variable. Why would a user
want to save that new value? You might toggle a (global) minor
mode several times during an Emacs session. Turning the mode on and
off doesn't imply that you want to change the saved value. I don't see
a use case for that.
If the global minor mode is at the state currently saved by Custom it
will not show up in customize-customized.
True, and if it happens to be in the opposite state, then it will show up.
I often put toggling of global minor modes in the menus.
So do I.
It seems conventient to me to be able to save the state of those
minor modes through customize-customized then.
I can see the use case you describe. I guess it depends on the use pattern
and the nature of the global minor mode. At least some mode toggling is not
tentative configuring, and at least some people might not want some mode
changes to be candidates for saving.
There may be no good way to satisfy all use scenarios and user preferences
for this. Another user option perhaps?