Theoretically, the keyboard can (but more than likely not) leave marks on the MacBook's internal display.glass This is why there is a very thin sheet of paper placed on top of the keyboard on a new MacBook out of the box. This helps protect the screen in case of keyboard or display assembly misalignment from the factory, especially during shipping (anything can happen).
The tolerances between the display assembly and the top of the keyboard are very small so Apple puts this protective paper barrier between the two.
In general use however, it's really not needed.
If on the other hand, you are actually seeing keyboard marks on the display glass, there is likely an alignment issue that should be made known to Apple.