I don't see much reason for it. The real problem is that the output is opto isolated from the line power. You can't get below the 1.7V the led needs to turn on without another external supply.
The opto is used for the 5V standby supply which works fine even if the main supply is unstable. I altered the feedback loop on pin 17 of the SG6105D to only regulate 12V and made it adjustable which works fine between 3V - 15V on the 12V rail. It must be something around T3 or its drive circuit which makes it unstable if pulses are skipped.
It actually was a similar problem. The input of the error amplifier (SG6105D pin 17) is compared to a 2.5V reference which makes the output unable to go below this value. At the extreme setting of direct connection of the output to the input of the error amplifier the psu gets unstable (maybe because it bridges the filters).
You could always add an LDO but that wastes power, very inefficient.
But then if you "synched" the LDO ref leg to your control over the ATX
Vout might be able to minimize power loss while still keeping solution
in regulation. Just a thought.
Regards, Dana.