My first post at Neogaf! I've broken radio silence after three years because of the infuriating misinterpretations in this thread.
Sticking felt / cushioning to the inside of the dock will INCREASE the potential for scratching the screen:
1. Over time, felt and textile materials can easily attract and hold dust particles. Tiny particles of dust can on a micro level be abrasive, sand like and scratch the screen.
2. Cushioning the inside of the dock with textile material will make the space in the dock tighter for Switch to fit inside, and thus magnifying the chances of scratching.
Having spent a few years working closely with industrial designers, I would say that Nintendo's decision not to include soft material in the dock is absolutely right -- even though this may at first seem unintuitive. As for the plastic of the dock scratching the screen, I doubt it and I'm sure this has been rigorously tested by Nintendo.