My perspective on the issue is that enrolling a user on a course using the mnet -> enrolment interface is the equivalent process to using the admin -> assign roles option within a standard course. To my knowledge, users do not receive a welcome email when they are enrolled in this way. They only receive a message if they are enrolled via the enrolment key option or one of the other enrolment plug-in options that allow you to choose whether an email is sent to students or not.
For this reason I consider the current default sending of an email as a bug for mnet enrolments. However, the fix shouldn't block all welcome messages from being sent. Instead it should focus on the trigger for sending emails treating mnet enrolments the same way as it treats users added manually via "assign roles" in the content provider course.
Of course this ignores the requirement we will have for some sort of bulk enrolment process for mnet users - but that's a separate discussion
Cheers
David