In this case the primary reason for configuring it as point to point links is that it matches the hardware topology. In theory there is a standards compliant way to create an ethernet-style network from this, but there are two critical software components to that that are not implemented in mainline kernels (namely raw Ethernet over TB and SPB).
The main disadvantage inherent in the physical topology is that you are always going to do switching/routing decisions on the CPU. But as long as you use that as a virtualization platform or run k8s on that you are going to do that anyway and the additional overhead is probably irrelevant. (This assumes the full mesh topology, which with this hardware is not scalable over 3 nodes, might be to like 5 with somewhat more expensive consumer grade HW and is not really scalable to more than 8 nodes due to the sheer amount of cabling required)
The main disadvantage inherent in the physical topology is that you are always going to do switching/routing decisions on the CPU. But as long as you use that as a virtualization platform or run k8s on that you are going to do that anyway and the additional overhead is probably irrelevant. (This assumes the full mesh topology, which with this hardware is not scalable over 3 nodes, might be to like 5 with somewhat more expensive consumer grade HW and is not really scalable to more than 8 nodes due to the sheer amount of cabling required)