Yes they can, both models. I'm convinced after seeing it on the various DS systems too that Nintendo does it on purpose to make money off repairs or new systems. I've had it get linear scratches that match the edge of the mismatch sized screens or where the circular pad sticks up enough to make contact. If they're close on a desk fine, but if you stick the thing into a snug case, a pocket, whatever, they rub. My 3DSXL had an unfortunate accident about a year ago, NOA through sheer kindness since the warranty was non-verifable for whatever reason still repaired it free. My screen inside was straight busted on bottom, but they replaced both the top/bottom and the notes noted the scratches so they wanted it fresh. If they did that other panel included I think they're just used to swapping them usually for a charge.
I always keep a flat folded over smooth cloth meant to wipe smudges off glasses inside the system when it's closed and it has never failed.
ZERO -- I couldn't care less about the face plates, but I want that model. Why? It's like $40 less. The battery life is just as nice. The system while like the 3DS in size, the screens have been slightly increased in size to be closer to what the old 3DSXL has. The smaller screen gives the intended proper clarity of the games. The New3DSXL model makes stuff a little less clear since it's blown up a bit, the new 3DS XL is even bigger than the XL while the screens are the same if I remember right and was done so for comfort concerns. I really don't want the New 3DSXL but NOA seems hell bent on forcing people to have no choice and pay more for no choice since the bastards have been region locking their handhelds since they added online with the DSi which sucks.