If you are running dual PSUs then PSU(1) that powers the motherboard should also power all the risers. The other PSU(2) should only power GPU 6pin/8pin. This configuration ensures both PSUs are properly grounded.
You must connect the SAME psu that powers the riser to the same GPU 6/8 pin 12V connector. The purpose of the power to the riser is to give a current boost to the PCIE 12V bus feeding the GPU (up to 54 watts), not to feed power back to the MB. If you have been doing it the way you described, only luck has been on your side. I know others do it this way as well, but this is actually wrong and is one of the reasons people have stated they can only run 2 risers on the same molex cable bus before it gets hot. It's overheating because the voltage potential between the molex 12v bus on one PSU and the 6/8pin 12V on another PSU is out of phase and causing a balancing current draw. But the part you said about not using the molex on the MB is correct.
Likely the reason why the OP burned up his MB is because he used the molex connector on the MB in the first place. You can't do this while using more than one PSU with the risers or GPUs. The reason is because of voltage phases with switching power supplies. He also may be on to something with one of the GPU PSU's being off and the MB trying to power the GPU alone, but this is a design flaw with all these Molex motherboards. There was never a provision for additional power to be supplied the way they are doing now. In normal circumstances, without the molex power being there, his MB would have simply shut down from an overload and prevented this hazard. but because that molex connector is running 12V on it's own bus, bypassing other circuits and thermal overload protections, it just ran away with the current. His PSU should have also prevented this from happening but the molex bus is allowed to do it's own thing and doesn't have the overload protections that the 24-pin bus has in place.
I'm an electrical engineer, and I have yet to understand how the MB manufacturers have got this so wrong. You can NOT use one PSU to power the risers and another to power the 6/8 pin GPU connectors with switching power supplies. This will create a potential delta of 12 along the same bus if and when one PSU is out of phase with the other on the same circuit. I don't think most people understand how a switching PSU works. It's basically a square wave cleaned up, but under heavy load it still shows itself as a square wave. For argument's sake, think of one PSU at a +12V peak for 60 cycles (an example, but it could be higher) and another at anything less than 12V or even zero, for 60 cycles on the same circuit. Whatever the difference is, the phase will create a voltage potential that shorts the circuit or the power bus in this case.
Do NOT use the molex connectors on the ASRock or Gigabyte mining boards. It is not necessary and is actually dangerous when using more than one PSU. It's a design flaw to even offer them. You would only ever need to use the molex connector if you had one single insane PSU run all the GPU cards and didn't use powered risers. I have been running both the ASRock and Gigabyte mining boards with 12 cards and have never used the molex connector on the MB.
I have read a popular post before from an "electrical engineer" making the same claims as you. The flaw is that most risers still draw power from the MB, if they didn't then you would be correct. Have you ever tested this out? If OP had the PSU powering the MB connected to all the risers, and the MB molex coming from the same PSU that powered the MB 24pin/12v. then he never would have ran into a issue.
I don't think MB manufacturers have got this wrong, I think you've got it wrong. Some boards will not post with more than 3-4x GPUs without a molex plugged in. It's only a problem if the molex you are using is coming from the PSU that's not plugged into the motherboards 24pin/12v connector.
