The backplate uses four 8643 connectors so if you use the hba for all 15 hdds, you will not be able to use the ssd. Unfortunately the 16th drive is not usable.
Set F
(2x) 2x SFF 8643 → SFF 8654 [2x Mini-SAS-HD (Backplane) to Slim-SAS]
You won’t be able to “also plug in an nVME ssd I will have in a caddy” to the HBA. There are 15 drive bays on the backplane and no way to access the 16th SAS channel. You would have to plug that into the motherboard.
You don’t mention the motherboard. Are you sure it will support a GPU and two PCIe electrical x8 slots for the NIC and HBA? I realize it’s an Epyc CPU, so it probably does, but you’ve got a lot of PCIe bandwidth going on in that build.
FYI, the number of lanes don’t change based on the PCIE generation. A card will use a certain number of lanes (1, 4, 8, or 16) based on a combination of the physical pins on the edge connector and the processor and chipset architecture (page 15). The PCIE lanes of SLOT 4 and SLOT 6 are shared. If you were to put your GPU in SLOT 6 and leave SLOT 4 empty, the GPU would use 16 lanes (the edge connector and the physical slot have pins for 16 lanes). When you put your GPU in SLOT 6 and the HBA in SLOT 4, the GPU will only be able to use 8 lanes, not because of PCIE generation, but because those two slots share the 16 available lanes to the CPU, so SLOT 6 will negotiate as 8 lanes and the HBA will negotiate as 8 lanes. Also, although the physical length of SLOT 4 is x16, only half the pins are electrically connected in it, it is only ever electrically an x8 slot. This is why in the manual they talk about SLOT 4 as “PCIe 5.0 x8 (IN x16)”. Your NIC has an x4 edge connector and your HBA has an x8, so those should operate at their maximum rated bandwidths in their respective slots.
Also, just FYI an LSI 95xx series HBA is overkill for spinning rust, you could use a 93xx series card for probably 1/3 the cost and see no performance difference. You may have other reasons for selecting it (already purchased, on sale, future move to an NVME array, etc), just saying for your build as is, it’s $200 or something and extra heat in the case that will have no performance benefit.
