Typical usage of this plugin is to keep the main site visible, only the subsites would then have an option to be less visible.
If everything is to be hidden, manual blog/user creation is best option, no?
At any rate, the plugin should not be causing the wp-signup.php page to be “unfound”. Something is amiss there. WordPress Multisite should redirect requests for the register page to wp-signup.php. Do you have other plugins altering reading/visibility settings?
You sure you have installed the plugin on a WordPress Multisite and network activated it?
Anyway, in my case, I want the plugin to have the option to limit access to new blog signup to logged in users. I do have a need to have the plugin limit new blog creation to admins only as well, but not the general public, subscribers, etc. During the season where signups to the public are open, privacy of the main blog is also public, then. When public signups are closed, I can still allow blog creation by members only, see?
Or delv into code by adding your own plugin to remove_action. Examples to do that are in the plugin already connected to wp-activate.php hooks.