We have 4U storage servers with X11DPI-N boards and we installed BPN-SAS3-826EL1-N4 backplanes and AOC-SLG3-4E4R retimer cards to connect to 4 NVMe U.2 drives via backplane.
In some servers we are getting random underperformance on some NVMe ports, which we cannot explain or solve by swapping cables, retimers or backplanes. (sometimes replugging the cables helps, but it's random, but we take into account the cables connectors might be worn out and perhaps some pins connect badly?) The poor performance on FIO test very often is assigned to a specific BAY (so also backplane port) and is 20-80% worse than on ports that are OK.
We have checked that AOC-SLG3-4E4R is not listed as tested AOC with X11DPI-N board, actually no retimer is on the list, just M.2 adapter. Have you ever tested that an NVMe retimer (2 port or 4 port, with oculink either oculink or miniSAS HD ports) does work properly on with this board and this backplane?
X11DPI-N was never built and validated as a 4U NVME system. NVME system is very complicated as it involved HW, FW, BIOS and device driver to get them working correctly. Since this is not a validated system, I don't have any document or suggestion to help you resolve the issue.