I brought this question up last week and @home is too slow now to do a search so I'll start a new thread.
I emailed the SE desk last night asking them this question and got a voicemail response this morning. (Talk about fast!)
They said I will defintely receive F or J COS bonus if I fly UA and upgraded myself using UA systemwides or any other form of certificates or miles. He reminded me that Aeroplan is one of the few programs that allow this.

He said that the system should automatically generate the COS bonus and if that doesn't happen, mailing or faxing in the BP would be sufficient to fix it up.
So looks like this is an added bonus for flying UA if one manages to find a way to upgrade!