How do includes/excludes work?
If no include paths are defined, all paths are included. After working out what is potentially included based on your filters, further paths can be excluded via the exclude filter.

I only want a cache buster for one CSS file
OK, add an '*' in the JavaScript exclude paths setting and enter the path of your CSS file in the CSS include paths setting.

I want to exclude all concrete5 files
Add to CSS exclude: /concrete/css/*
Add to JavaScript exclude: /concrete/js/* and /ccm/assets/*

Note: if you also use the concrete5 updates system or you don't use pretty URLS, use an asterisk (*) in front of the paths. E.g.: */ccm/assets/*

How does it work with Full Page Caching is enabled?
If FPC is enabled, the complete HTML output is saved and loaded the next time the page is requested. That means it bypasses any concrete5 events, including the cache buster. In order to cache bust pages that are in the FPC, flush the concrete5 cache or wait until the page(s) expire automatically.

Should I be worried about performance?
Two regexes are used against the page's HTML output. Normally this would hardly have an impact. But if you're worried about performance, you can enable the 'Logging' setting to test how it takes to add the cache busters. In my experience, the added PHP execution time is negligible (around 0.5 milliseconds). But if that's a concern for you, you'd disable the add-on and append the Config::get('cache_buster::settings.hash') manually to your theme's CSS or JavaScript file(s).

Query strings and proxies
Some proxies don't see query string changes as a 'new file'. Some people even advocate for another approach, e.g. style.123.css instead of style.css?123. This approach isn't implemented in Cache Buster, as it would require a change in your webserver configuration. If that change isn't made correctly, it'd result not-loading assets, which might even break your site. If you really want to use the other approach, you'd easily apply it manually to your theme of course, by using the method described above.