The GPUs might care quite a bit about bifurcation. The RTX Pro 6000s can communicate directly between themselves over PCIe 5.0 16x and saturate the bus doing so. This is used when doing tensor parallel LLM execution for the All-Reduce steps.

Someone can work around this by including a PCIe 5.0 switch like the Broadcom PEX89048. That switch can be used to, for instance, have the two GPUs talk to each other at full PCIe 5.0 16x speeds, while talking to the motherboard at say PCIe 4.0 16x, or even 8x. As an end user, cards using that switch seem to be an AliExpress only item, but I assume an OEM like System76 could get their hands on it to place directly on the motherboard. I imagine the price of adding that to a motherboard could be less than the price of switching to a Threadripper or Xeon 600 platform.

However, I can't find any evidence that System76 has added a switch, and in fact they refer to x8/x8 multi-GPU support, making me think they didn't add a switch. To my mind, this isn't a very satisfactory setup.