One possible way this can be done is by changing the 'ForegroundColor' property of blocks.
For example, you can add a 'Tag' to blocks. Tag can be added by right clicking on the block and selecting 'properties'. You can add the tag 'Controller' for all controller related blocks and the tag 'Plant' for all plant related blocks.
Then, you can find all blocks with 'Controller' tag using "find_system" command. For example,
>> controller_blocks = find_system(gcs,'Tag','Controller');
This will return a vector of handles to blocks which have 'Controller' as their tag. You can then set the 'ForegroundColor' property for all these blocks to white or some light color.
>> for i = 1:length(controller_blocks),
Same can be done for all blocks having 'Plant; as their tags.
For signals, I am not very sure how you would differentiate between 'COM' signals and 'physical' signals. Maybe you can do something similar after getting 'line_handles' for corresponding signal.
I hope this helps.