I would like to add that this warning is uncalled for. I have personally tried this plugin on several sites and never experienced the problem the OP is scaring people of. In the case where the plugin could brake something ( for example if you combine it with a cache plugin, my personal experience is that wp-super-cache plugin tends to crash the whole site if you move installation and needs special attention to reconfigure ).
Also, if this plugin did make any problems, I do not understand how it can still create problems if you disable it or even better uninstall it as all changes are gone?
I believe your problems is some other plugin and not this one, correct me if I am wrong.
On your last note – WP is free software and so is this plugin. The problem with free stuff is that you never have anyone resposible for making things work – I think the author if this plugin is rather reasonable in answering all comments. If you want something you do not need to try I recommend purchasing a proprietary CMS – I can recommend my own system Easy CMS ?? But lately I have been having more fun with WP as everyone theese days want a piece of the free wave… All those tasty templates and plug and play!
In my experience I have rewritten alot of plugins to fit my needs, but I keep reminding myself when it comes to this plugin that the effect you get for just enabling it outweights by far the time needed to custom optimize a site looking at actual worth in real word!
I wish this plugin wasnt so damn effectful, but it is! And by the looks of it its suddenly gonna become even better as the author and people are being reminded of possible problems when combining the CSS for screen and print as example, and google page speed aswell. At the moment everyone should use this plugin as a default plugin in WP – unless you custom optimize everything that is!
If this plugin was a woman I would date her! Haha!