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.
The jumper isn't signalling a motherboard is connected it is signalling the power supply should supply power to the rails.
Overvoltage into a motherboard is just as bad as overvoltage into any other device. You are replacing one device which will be destroyed by overvoltage with another device which will be destroyed 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 is designed to do exactly that. The sole purpose of the power supply is to ensure that the output remains within a range (usually <3%) around 12V nominal. Please show me in the ATX power spec where a power supply is suppose to shunt overvoltage into the ATX connector. Please show me in the ATX spec where a motherboard (a device vulernable to overvoltage) is designed to be the dump for excessively high voltage.
It is complete and utter nonsense. 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 there is excessive voltage it is the responsibility of the powersupply to either regulate it or disconnect the load (connected devices). Yes power supplies contain overvoltage, overcurrent, and overheat protection circuits. The powersupply (not the motherboard) monitors the voltage, current, and its internal temp and the powersupply not the motherboard kill the current if it is out of spec. 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.