I had the same problem with a motherboard integrated nic, I think it's because I haven't find its DEV-BUS yet so at each reboot, qnap loader finds a "new" NIC when checking hardware available. You can verify in Qnap UI network panel, the network card obtains a new number at each boot (increment by 1) .
I've solved this problem by disabling integrated nic and adding a pcie network card in a slot I know the DEV-BUS address and modified, in model.conf, the [System Network 1] DEV_BUS=Bxx.Dxx.Fx accordingly.
Now, the mac address is always the same and there's no more duplicated nic in qnap network menu.