Mine is a bit bent like that too. I think that's normal?
So... I tried a couple things to ensure my screen doesn't get scratched.
First... I tried taping a couple soft screen cleaners to the inside. This made the Switch slide in pretty tightly, and I worried that if any dirt or dust got on the screen cleaners, that would probably cause scratches too because it was so tight.
So instead... I ordered one of these...
https://www.amazon.ca/gp/product/B01FM4ZQLQ/
It came in this morning and it works perfectly and doesn't look half bad either. Now my Switch can sit outside of the dock and have more ventilation too and have zero chance of being scratched by the dock.
Pretty ridiculous that we need to jump through all these hoops. Joys of jumping in on day one I guess.