If a site owner goes to upgrade, the admin menu that appears at the top will have the name of their site. However if they click that link, it takes them to the network wp-admin area with a message saying they don't have the right to be there. This is because your workflow has them go to the register page on the main site.
So to register they go to
If they then click on "My Sites" in the admin bar, it links to /wp-admin but not from their own site. This is generally an issue because anytime the user is logged in and they visit the main site, they will have this errant link.