I didn't say the riser is pulling 12V from the motherboard, that's not the point. As I showed, it's the fact that the riser IS sharing an electrical connection with the motherboard and all electrical connections to the motherboard must come from the same power source to avoid conflicts in regulating the voltages from having different power sources.
Ok, fair enough. But the 3.3v is created from the 12V through a regulator on the top side of the v008 board. Even if this were electrically shared with the 3.3v bus on the MB, it is regulated and isolated from the Riser PSU via the 3.3v regulator on the riser board. The riser does not use 3.3 from the PSU, in fact it converts switching 12V to regulated 3.3v. This isolates the riser PSU from the MB 3.3v and PSU, therefore there is not harm in having a separate PSU on the riser from the MB. The problem is not with sharing 3.3v power from two different components on two different PSU's, that is actually safe because of the regulators and low current parameters, and the power is no longer switching. Small potential differences of 0.1v is not going to short out or ground the 3.3v circuit. The real problem is from sharing direct
12V Switching Power and this is where the danger and the fires start.
You absolutely 100%, without a doubt, want to power your Riser with the
same PSU powering that GPU 6/8 pin 12V, this is a fact. If you don't, this is where the danger arises. Internally the GPU is drawing 12v Switched power from two sources if your riser is on a different PSU, and that's a big red flag. What's the point in worrying about the isolated, regulated, low current 3.3v MB to Riser connection when you are mixing pure high current 12V switched power right at the GPU? If one switched PSU happens to go 180 degrees out of phase from the other switched PSU on the same 12V circuit, bye-bye. This is likely what happened with the OP. We don't really know how he was setup, likely two PSU's on the same MB for all we know, but had he simply left the Molex disconnected on the MB, he would not have fried it.
I don't know who decided this was the rule to use the MB and risers on the same PSU, but electrically it's wrong to mix PSU's with the Riser/GPU combo, and it's electrically safe to have the MB powered by it's own PSU separate from powered risers when switched 12V is not involved.
Friends don't let friends put Risers and GPUs on different power supplies, remember this!
Part of my past applied studies were in voltage regulated circuit design, I'm not speaking out of my arse here, I know what I'm talking about.