I tried to capture them with my phone's camera, but not being a photographer I couldn't get the scratches in focus. Fortunately, I found a picture of someone else's unit, with nearly identical marks:
Lo and behold, I got home and inspected the dock: as it turns out, if you view it exactly from the side, it's visibly bent inward at the top-- as in, the opening's distance at its peak is much smaller than at the bottom:
For better visibility, I removed the "joy-cons", and from a profile vantage, I slid the Switch into the dock as slowly and gently as possible-- and sure enough, the plastic rails for the entire first third or so of the system's travel make continuous contact with the screen as the system lowers. There is no way to avoid the contact-- it's physically too tight of a fit.
I think I know the cause too: the front panel has a discrete, inner piece of plastic-- and if you bend the outer portion of the dock outwards with your hands, it flexes along that crease. I think during manufacturing, some of the docks' screws-- which hold these two plastic items together-- were torqued too much. You can reproduce this easily with other materials: even take two pieces of wood, and join them with screws so they are perpendicular: if you over-torque the screws, the vertical piece of wood will start to warp towards the pressure.
Frankly, I don't even care that my unit has scratches, and am going to just keep using the dock anyway; I can just manually flex the plastic outwards with one hand, and use the other hand to maneuver the system.
If I get adventurous, I may try removing the front panel altogether, although Nintendo insisted on using these really bizarre "safety" screws, for which I lack a driver. Which is why I prefer PCs-- they are 100% standardized and modular. In fact, most of them are "tool-free" now, with the proliferation of thumb screws.
But despite my apathy, I can easily see others with bent docks never buying a Nintendo product again because of this issue.