There's a couple disadvantages of running the two plugs on one cable though.
- Two separate 18AWG cables will have almost twice the surface area to dissipate heat from vs one 16AWG. That's why you see ampacity in a cable go up only 56% when you move up three gauges even though the resistance halves. Flat cables help with this, of course.
- Two plugs on a 16AWG cable pulls the entire cable current through the Minifit Jr on the PSU side. At 200W per cable this isn't terrible, but it's still a significant difference. At 17A per board that's 5.67A per pin vs half that with separate modular cables.
- Worse fault tolerance. If you're running one cable and one pin/wire is compromised for whatever reason, you can then be pulling the full 17A through just two pins, which is over spec. If you're running two cables and one pin/wire gets compromised, you're now pulling the 17A over five pins which is still fine.
I would say two plugs on a 16AWG cable is closer to two plugs on an 18AWG than two separate 18AWG cables even if just the wire resistance seems to show they're comparable. A lot of these issues aren't a problem two plugs on a fixed 16AWG cable though. If you find yourself with a supply that has two fixed dual plug cables and four modular dual plug plug cables, use both plugs on the fixed cable and a single plug on each of the modular ones to make up your eight plugs.
Not that the RM1000 won't work, but unfortunately not all 1000W PSUs are 16AWG on the PCIe cables. For instance the otherwise excellent rated Cooler Master V1000 uses 18AWG on its four dual plug PCIe cables. In most cases even dual plugs on 18AWG won't cause an issue, but you're still more likely to melt a plug at the PSU with a modular dual plug cable than with separate cables.