Gadget checkboxes should be able to be grayed out (inaccessible) dependent on if another gadget is on or off, if other extensions exist that gadgets are unable to use, or if they require a specific skin to work. For example, on en.wikipedia the current "Editing" section of the gadget tab on the preferences page looks like:
commons:File:Special_Preferences_mw-prefsection-gadgets_(current).png
There should be a way to gray out functions, like:
commons:File:Special_Preferences_mw-prefsection-gadgets_(proposed).png
If (in this instance) VisualEditor is enabled.