I guess this is not how it's supposed to work. What I think? Compared to your minibb-forum I notice a difference, which is that in your email notification (like I received for this topic) there is a www-link, while in my email there is an m-link. Maybe that explains how it works differently on my forum.
Yes, it would mean there's a little mess with $main_url
option in your setup_options.php. Make sure this setting is not repeated in a generic manner in this file. Email notifications should be sent only for the primary/basic forum domain (of course, if you have not redefined this rule in email templates - you may check email templates as well for making sure they forward to $main_url
Yes, it's correct that if you open m-version directly, you are suggested to enter the mobile forum only. That's how it should work.