Good post CC;
Having spent a good deal of today dealing with this incident, I feel qualified to discuss it (although not allowed to).
But...
The B737 got traffic, the Golden Eagle called, the BE20 got pushed down to get out of the way.
The VFR Golden Eagle did call for a clearance VFR through C (inside ML TMA) for ADES YMEN; this was not available for many reasons, including inclement weather. So the GE requested an IFR clearance.
This is why it is complicated, not only is it a VFR and two IFRs, it's now possibly three IFRSs.
I can safely say that the ATC involved not only had a sleepness night; but so did many of his colleagues. (Including me)
Calmness over the air, maybe it is because he's a professional, total wreck emotionally is another way of describing it... Everything is OK hey SNAREK, shame on you and your kind.
This is a totally NAS realted problem; the aircraft involved got 'over serviced'. The C421's transponder wasn't showing mode C until he recycled it as part of the request a clearance procedure and subsequent identification, hence the TCAS (RA) trigger.
The ATC involved did an outstanding job, fact.
The system is absolutely dangerous, as predicted. It only takes one small error, such as this type of transponder issue and all the system defenses (sic) are gone.
They would have been a very close miss (or hit) if the VFR had of requested his clearance ten miles later. He's only required to call at 46 ML, he requested it a 65 ML... As it was it was 1NM and 400 feet...
Luck saved the day, lets hope we stay lucky.
John Anderson, stop this and stop it now, you have been tragically miss advised. "in contact with the tower" indeed, you fool.
Bottle of Rum