From what I've read online, Dell does something similar. There's some sort of card/add-on that can enable directly seeing and booting from PCIe but they are costly.
This server has the internal USB and a build in SD slot accessible from the rear. (There's also a dual card option like you mention for redundancy.)
My plan was to get Clover working with USB, then use the vFlash SD slot to hold the Clover bootloader in read-only mode. This would hopefully prevent the SD card from dying quickly.
I don't think the bifurcation is causing me issues. Before I enabled it, I wasn't able to see the drives from iDRAC/Bios. From what I've been able to research, this is expected and Dell sells the "solution" to booting directly from them. (Add-in card that's pretty pricey...)
I do have an old SATA SSD that I'm considering slotting into one of the bays and using to boot. But I see that as a "last resort" option. I was hoping to have a bit of redundancy with the Proxmox install/configuration itself.
I feel that there's a solution to the current setup and I just lack the knowledge to fix it. Everything I've been able to find points to my current setup being able to work. I'm just being hindered by not understanding partition/device/boot structure.
From what I understand, and what I saw during the Proxmox installation, if I can get past whatever part of the POST/boot process is preventing seeing the drives directly, I can use Clover to bootload from there. I've been able to boot into Clover just fine, and it was able to "see" the drives and partitions. I just don't know which one should hold the Proxmox boot and if I've configured the Clover config correct.