There is no Apply button in the Preferences panel. The settings panels have the Apply buttons, and I am not suggesting they be made non modal for the reasons you state. Some of the panels can be accessed without going through the Preferences panel**. That suggests to me they could be in a calibre toolbar/menu like everything else.
** Look and Feel->Tag browser/Book details/Cover grid/Cover browser/Quickview, Add your own columns, Searching.
The Windows Control Panel and Settings tools are also icon grids but unlike calibres Preference icon grid they are keyboard accessible… as is calibre's cover grid, which to my mind is a far more complex object than a fixed icon grid.
BR
|