Multisite Custom WP installation folder

I have a WP multisite with custom WP installation folder. I did these following steps as suggested by WP Codex:
1. Installed WP normally in domain.com
2. Set the siteurl to domain.com/wpfolder, followed by a proper editing on wp-config.php and .htaccess.
3. Moved WP files to domain.com/wpfolder
4. Activated WP network

It works, and I can make and manage new/sub sites normally. However, it is odd because I can administer the main site using two URLs, i.e. domain.com/wp-admin and domain.com/wpfolder/wp-admin, and manage the whole site using domain.com/wp-admin/network and domain.com/wpfolder/wp-admin/network. What really happens? It seems that there is an improper and incomplete redirection procedures. What should I do to completely move the mainsite and network instalation to the domain.com/wpfolder?