In a multiple PSU setup the reason you want to connect the risers to the the same PSU as the motherboard is because all devices connected to the motherboard MUST share the same power source and ground so the voltage can be regulated according to a single source.
https://bitcointalk.org/index.php?topic=1843586.msg18351224#msg18351224The problem with powering more than two risers per molex strand is 18 AWG wire is only rated for 10 A max for single core wire, which is 120 W at 12 V and much less for multi stand wire. Using more than two risers per PSU cable strand WILL exceed the rating of 18 AWG wire, causing the wire to heat up and is dangerous.
https://www.engineeringtoolbox.com/wire-gauges-d_419.htmlWell, I disagree with this. It is more important to run the same PSU powering the riser and the GPU than it is to worry about MB to riser ground. The PSU, Riser, and GPU ground need to be tied together but the MB does not need to be on the same loop when using a powered riser. The reason is because the MB power is not powering the riser or GPU at this point. The USB cable is transferring data, not delivering 12v power, therefore common ground is less consequential.
On a side note, I have run 4 risers (Titan XPs) on one 18 gauge Molex and the current draw was not even 10A as long as the same PSU powered the GPU 6/8 pin. I'm not saying it's best practice, but as soon as I separate the PSU that powers the riser from the one that powers the GPU, the current draw goes up and the Molex bus gets hot. This indicates a voltage potential difference on that bus, creating a greater power draw on that Molex bus. If the riser power is on the same bus, most of the power will be supplied via the 6/8 pin connector. While PCIE standards allow up to 75W via 12v and 3.3v combined power, most cards are designed to only draw up to 35 watts via 12V and the rest comes from the 6/8 pin bus.