A restore destroys the existing VM when restoring as the same VMID. Then it creates a new VM based on the backupped virtual disks. Passthroughed disks are not part of the backup, so they won't be part of the newly crated VM. Similar thing with virtual disks excluded from backup. Those also won't be attached to the restored VM but show up as a unattached disk.
But don't ask me why they did it that way. My guess would be that you could restore the VM on another node where that physical disk then might be missing so the VM won't refuse to start as the disk can't be found.
The config file is already included in the backup archive.
How I solved it:
You can write a note to each VM. I added the "qm set ..." commands as a note. So after a restore I just copy the commands from the restored note and paste it into the PVE nodes shell to add them again.
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