according to Several warnings on boot those “supply not found” warnings should be ok
i think the " brcm-pcie fd500000.pcie: link down" means there is nothing connected to the PCI controller. In case you haven’t aimed to connect something via PCI this should be also fine i assume. Especially, since the PCI and USB host controller are fully independent on the CM4 (in comparison to the RPI 4 Model B, see section 2.3. in the CM4 datashet).