This plugin protects your WPMU signup process against spambots with a simple math question.
Yes, you can run both. I use the regular WordPress plugin on my WPMU site as well to allow individual site owners the option to add the protection at the blog level.
No. This is only targeting the WPMU new blog signup and new user signup functions. If you need WP registration, login and comment protection I recommend you get the Block Spam By Math plugin.
Yes, just edit the two rand functions in the plugin file to generate whatever type of numbers you want.
Yes. Requires Buddypress 1.2.7 or higher