A:AnswerYes, I use a matte cover (for glare control) and have used other screen protectors with absolutely no problems (including the tempered glass variety). Just keep the inside of the cover clean of any debris, and you shouldn't have any problems.
A:AnswerNo, there is no place to attach the Apple Pencil. This is simply a luxuriously thin magnetized cover for your screen. It is not a front and back CASE. It’s awesome, but doesn’t sound like what you want.