The capacitive film layer of Kindle Paperwhite is under the light distributing layer.
The light distributing layer is on top and should be just as vulnerable to scratches as on Nook. However, Kindle Paperwhite is too new for many of such problems to have developed already.
The capacitive layer is considered to be 90% transparent (according to wikipedia), so there is an additional 10% loss of contrast on Kindle Paperwhite (at least 10% loss of transparency). As to the light distributing layer lowering contrast - it is well documented.
So Paperwhite loses most with two additional layers on top of e-ink.
I suggest buying Sony PRS-T2. Sorry, I meant some other Onyx Boox i62 which does not glow
Using this built-in lighting regularly is very unhealthy anyway. It should be used for emergencies only. Never at home, at least, where you can design and control your lighting.
Did you ever see a glowing in the dark printed book?
When the light is on, e-ink loses its purpose, you can use an LCD tablet just as well.
There is also an unhealthy tendency to use this lighting all the time so that the screen looks whiter.
I'd rather have a very compact but very good clip-on light in my pocket for emergencies (such as Ozeri Kandle II) than a contrast reducing permanent layer.