How is having a disc inserted into a xbox that is upright likley to damage it?

Gravity

It puts more wear and tear on the drive. When a disc is flat the load is evenly distributed, when it's vertical it goes up and down hill.

That's the short version.

Thank you for the answer, would you be able to explain to me what load means and what parts of the disc gets damaged?

Then you can potentially damage the disc drive as it’s not designed to operate upside down, and you should not have a disc in it if you were to do that. I recommend always standing it upright for most efficient cooling.

Scratching noise could indicate the fan has been damaged, has come loose or just at a strange angle. have you tried turning your Xbox on its side or standing it upright? Be sure to remove the disc inside before changing its position as that could damage
the disc if left inside. If it is still making the scratching noise contact support.

If it was sent to your by signature required courier (which it should have been in the first place), it pays to unwrap, unbox everything and check. Sure this may waste a busy courier persons time, but part of their job is to ensure the device arrives in
one piece to you. If it looks damaged, note that when signing for the delivery. If you don't note that it was damaged, the courier company is not liable for damages which occur in transit.

Yes getting things repaired is a big hassle. It could have been a software glitch. Try restarting your console (cold start). I know sometimes my disc drive does the same thing too. Just take it out put it back in again. After a few goes, it should be reading
your game discs fine. I think they went with a cheap Philips disc drive in original Xbox 1 consoles, that's why the original Xbox 1 consoles are not designed to be placed upright, because of the choice of disc drive Microsoft made. But with the Xbox 1 Slim,
it is designed to be placed upright because Microsoft probably went for a different/better disc drive.