Different motherboards will also kind of determine the overclock potential for the GPUs.
No they won't. Why would they? For CPU overclocking yes, there might be slight differences due to different VRM setups and the BIOSes using different approaches to configuring some parameters (different vdroop and LLC settings, for example), but what does the motherboard have to do with the GPU overclocking? All that matters (besides the obvious silicon lottery luck) is the power quality (PSU), and even that doesn't matter too much provided that there's enough power (unless the PSU is total crap). Never ever have my GPU OC results depended on the platform the card is used on, and that's 100+ GPUs and at least 20+ boards over the years.
So benching your cards in a test system will give you a good reference point, but it most likely wont be identical when you swap it to its home system.
What makes you think so? Have you ever had (repeatable) cases of one card running fine with set OC on one board and not being able to run with the same OC on another? With exactly the same PSU and not a faulty board? Excluding some nonsense of course, like reference rx 480 cards drawing more than 75W from the PCI-E slot, thus crashing on some boards and running better on others. In normal conditions, without anything like that?
