hansennn My box only had one protector. It's a rubbery kind of film.
As the time of my Moto G I was not using a Skinomi, I was using a Techarmor, and yes, the update to Marshmellow gave me eye strain even with that screen protector on.
My current phone has a Skinomi on it and I have blocked the Marshmellow update, so I cannot comment in whther or not it will help