Actually if you do main computer install in order to upgrade, yes AC will try to look for an instance of SQL Express 2005 and if it doesn't see it it will try to install it automatically. And if you are running 2008 SQL you will have an issue. But there is a work around.
I think the ultimate solution would be to have an installer/setup with the option to deselect things like bonjour, web server, sql etc... And have the typical for regular users.
