Some SideKick options (e.g. "tree selection follows caret") are mode-specific, and have a global default.
The main option pane of the plugin (under Plugin Options) provides the interface to the global default only, while the mode-specific option pane (available from the dockable) provides the interface to the mode-specific properties (as well as the global default).
The main option pane should also include a "mode-combo" using which the value can be set for any mode (including the global default). This will also make it clear to the users that these are mode-specific options that can be overridden per mode.