Well, if the exploding caps are caused by voltage buildup on disconnected leads after the miner is disconnected, even with the power supply off, the voltage buildup due to voltage memory of the capacitors, voltage buildup that the power supply designers decided would be drained by the motherboard, then the jumper is signaling a condition, motherboard connected, that does not exist.
Where would the overvoltage go in the motherboard. You are replacing one device destroyed by overvoltage with another device destoyed by overvoltage. Motherboards contain filtering capacitors on their input voltage leads, just like mining boards do, just like GPU do, just like just about every electronic device ever made does.
Any regulating powersupply does exactly that REGULATE the voltage. The sole purpose of the power supply is to ensure that the output remains within a range (usually <3%) around 12V nominal.
No power supply is designed to dump dangerous overvoltage into the ATX connector to let the motherboard "handle it". What would be the point. The POWER SUPPLY is the place to regulate voltage. If the motherboard was going to regulate the voltage then there would be no need for a power supply you could just connect your power cable directly into the motherboard.
The motherboard isn't expected to be normally unplugged. The voltage wouldn't build up with the motherboard connected, instead the capacitors, filter capacitors, are discharged thru the motherboard. No buildup.
Looking at the switching supplies recently that are used in USB hubs, switching supplies' voltage is regulated while the circuit is a "current mode" device". The flow of current allows the voltage to be accurately assessed and regulated. When the switching supply is looking at an open it may not actually measure or control the voltage.