I mean that you can make changes to the VM configuration file in the /etc/pve/qemu-server/ directory on the Proxmox host. The Proxmox web GUI changes are stored in the VM configuration fileThank you, you mean manually activate PCI Passthrough ?
/etc/pve/qemu-server/100.conf
(for VM 100). If the Proxmox web GUI does not support something, you can always use the qm program or change the file yourself.