Code:
0000:00:0e.0 RAID bus controller: Intel Corporation Volume Management Device NVMe RAID Controller
VMD is basically a PCIe bridge.
Code:
10000:e0:06.0 PCI bridge: Intel Corporation 12th Gen Core Processor PCI Express x4 Controller #0 (rev 02)
10000:e1:00.0 Non-Volatile memory controller: Micron Technology Inc 3400 NVMe SSD [Hendrix]
These devices are behind the VMD bridge.
If you disable VMD in the firmware setup, you should be able to enumerate all PCIe devices like normal. If you can't or don't want to do that, you'll need to write a driver for VMD to access devices behind it.