Disable user registration in /user/register, but allow registration during commerce checkout? Only users who paid can finish registration and they get a role applied to their user.

Problem is that, users can still register through default registration form.

Disabling registration for in Account settings will disable the registration globally everywhere?

How to disable it only in /user/register? But allow during commerce module checkout process?
You can do that with hook_menu_alter() by changing the access for that path:

function MYMODULE_menu_alter(&amp;$items) {
  $items['user/register']['access callback'] = FALSE;
}