A plastic screen was the proper design choice because of its ability to flex and not shatter. The idea that there is an issue with the dock design has some merit as you are repeatedly sliding the unit in and out of it, and although it isnt overly tight, has a decent tolerance. The plastic rails however, are not in the viewing area of the screen. Rather, they slide over the black non viewable bezel on either side of the viewable portion of the screen.
Although I personally like the look and idea of the psp docks, the reason for the Switch dock design choice I believe, is simple. The console is sandwiched in the dock and far less likely to get knocked over/off the dock and be damaged. It has nowhere to go unless someone yanks a cord or slaps the whole dock off the tv stand. I also believe it's shape and size (on the back) gives Nintendo the ability to make much speculated add in hardware that could utilize the usb 3.0 inside the dock
The answer to this whole debacle is pretty simple and costs around $11. A Hori screen protective film.