Sorry I would not be able to help with mods or hacks. I would have no idea any issues regarding those since I would not be using them personally. vbulletin.org has thousands of mods and there are tons of issues with using hacks that are covered there. it would be up to the hack authors to resolve any issues with there coding. Just like Internet Brands the makers of vbulletin we do not provide support for mods.
Our application is written to integrate with a clean stable vb4 code. I am not aware of any issues with the css and we do load the additional css stylesheet. As always any custom styles may or may not cause issues which would have to be discussed when found. additional.css is where you define additonal classes and if you use those classes in the header or footer they should show fine on our application. Our application itself should not be affected with any custom classes you use since our templates use the standard vb