So to close the loop on this one, I actually ended up using a different grunt tool that essentially accomplishes the same goal called purifycss. I was able to target purifycss at the craft template folder, get it to look at bootstrap css selectors actually in use in the templates, compare it to the full bootstrap css files, and then have it output only the css that was being utilized in a final minified css file.
It ended up being that I was only using about half of the available bootstrap css selectors so it cut a bunch of unused css out of a very large file.
Also, I believe I could have taken the same or similar approach with uncss so if you prefer that tool, I believe you can use it in the same way (though I did not personally so can't speak in detail to it).
Here is the excerpt from my gruntfile.js: