Ryan,
Could you put together an example of a theme rule that would highlight the spaces in a document using this bundle?
Just add a new line to whatever theme you are using (in prefs, fonts&colors, click the plus button), select that line, enter the scope selector that the Invisibles.bundle assigns to invisibles - et voilá!
hth,
Daniel
PS: I don't have access to the bunlde -- thus you will need to figure out the scope yourself from the bundle editor.