I have SYS-740GP-TNRT (BIOS 2.1, BMC: 01.05.03) that when I'm trying to do PCI-E passthrough for the NVME drives in the U.2 slots for this system, it encounters the following error running Proxmox 8.4.1
kvm: -device vfio-pci,host=0000:65:00.0,id=hostpci0,bus=ich9-pcie-port-1,addr=0x0: vfio 0000:65:00.0: Failed to set up TRIGGER eventfd signaling for interrupt INTX-0: VFIO_DEVICE_SET_IRQS failure: Transport endpoint is not connected
TASK ERROR: start failed: QEMU exited with code 1
Upon inspection, I've found these devices were not assigned an IRQ number. Kernel log
[ 5.106155] nvme nvme0: pci function 0000:65:00.0
[ 5.106165] nvme 0000:65:00.0: PCI INT A: not connected
[ 5.106192] nvme nvme1: pci function 0000:99:00.0
[ 5.106398] nvme nvme3: pci function 0000:68:00.0
[ 5.106407] nvme nvme4: pci function 0000:9a:00.0
[ 5.106410] nvme 0000:68:00.0: PCI INT A: not connected
[ 5.106784] nvme nvme2: pci function 0000:66:00.0
[ 5.106790] nvme 0000:66:00.0: PCI INT A: not connected
[ 5.106990] nvme nvme5: pci function 0000:67:00.0
[ 5.106996] nvme 0000:67:00.0: PCI INT A: not connected
Once you setup SR-IOV in the BIOS and boot into OS, everything else is control by the kernel through linux nvme driver.
You can try other linux like Rocky/RHEL 9.5 which has the latest nvme driver and see if you are having similar issue or not.