I have pro-sites network activated. I then went into the premium-plugins admin page and set one of my plugins (foobox image lightbox) to auto-activate. It was also set to 'anyone'.
So I used a customer username, went in and created a new website and found that the foo plugin was not activated when the site was activated.
*I even went as far as to setup a default template for new sites, and had the foo plugin activated and configured on the template site just in case that plugin somehow took priority. While the plugin didn't activate automatically, the other settings from the default template site did work.