I've had mixed success using the JS and CSS combine and compression tools. The main problem seems to be with using Google's external jQuery library instead of compressing it with my other scripts. One way to increase support for such irregularities might be to support a html comment placeholder for where to place the generated files. WP-Minify allows for a <!-- WP-Minify --> comment for instance. Otherwise, I can't think of how I might get this feature working.