Although there isn't any way to change the default background color, you can write MATLAB code that will find all of the annotations and set their background color. Unfortunately, this would still be a user-driven action, not something automatic (i.e. you would still need to actively run the MATLAB code)
The MATLAB "find_system" command can be used to find all of the annotations:
annotations = find_system(sys, 'FindAll', 'on', 'type', 'annotation');
From there, the "set_param" command will allow you to assign a new color to the annotations:
set_param( annotations, 'BackgroundColor', 'blue' );
