Dell R740 is a skylake CPU system. Skylake processors from Intel introduced the possibility for multiple PCIE root complexes on a single CPU. Previously, intel Xeon processors had a single PCIE root complex to which all the PCIE lanes were attached. This is no longer the case (with skylake).
PCIE traffic flowing on a PCIE fabric connected to a single root complex is what is normally required for proper P2P usage and is what the nvidia-smi topo -m tool will report as a PHB link.
Previously, since such a statement was equivalent (because of the 1:1 correspondence between PCIE root complexes and CPU sockets) to saying “PCIE devices attached to a single socket”, that was commonly the heuristic for determining whether P2P traffic would be supported between 2 PCIE endpoint devices.
However, PCIE P2P traffic is not, by definition, supported between PCIE endpoint devices attached to separate PCIE root complexes, whether those root complexes are on separate CPU sockets (as would have been the case historically) or on the same CPU socket (as is now possible with Skylake).
Therefore, at the current time, your nvidia-smi topo -m output is the expected behavior for that system, there are no BIOS settings that can modify that, and you should not expect P2P behavior at the current time between devices attached to separate root complexes.
It’s entirely possible, of course, that a “technological breakthrough” could occur (let’s say between NVIDIA and Intel) that would allow for sufficient information exchange to occur so as to document the method by which P2P PCIE traffic could be reliably supported between PCIE endpoint devices attached to separate root complexes, but such activity has not happened yet, to my knowledge.
You should be able, with sufficient effort and knowledge, using a linux tool like lspci, to confirm the outlines of the above assertion, in particular that the GPUs in question are attached to separate root complexes. You should see lspci enumerate multiple host bridges, and with the tree display form of lspci, identify that the GPUs in question are attached to separate host bridges.
Since this is a Dell platform, I’d also encourage you to get in contact with Dell for confirmation of this and/or further support inquiries.