...why work with the HC Office at all? From the issues stated, it seems like that would have been something for an academic counselor to handle—or even his professors, department heads, etc.

In the case of the latter event, tha too sounds like something better left in the hands of ecclesiastical leaders and probably a good attorney.

I’m happy to hear that these things worked out for your friends—successful outcomes from the less-than-perfect while at BYU are encouraging. However, it’s rare (or nonexistent) when I hear something in which the HC Office has been involved where it doesn’t seem like a rendundant department. I wouldn’t counsel a friend or loved one to seek them out on either of those cases if there were a choice.