-GtkCheckButton-indicator-size, -GtkCheckMenuItem-indicator-size and -GtkRadioButton-indicator-size (and the corresponding gtk2 settings) seem to be ignored: Checkboxes and radio indicators are always the same size. This is a problem on high-res (full HD) notebook displays: The default size is by far too tiny.
This is a result of the way the checks are rendered (this comes from gdk rendering). With cairo rendering this can be improved. As you state, with the high-res this seems like a good enhancement.
Implemented in commit ad461c4