Clarity definitely will be affected for every screen protector pasted, be it Glass SP (less affected) or TPU or hydrogel (more)
Of course, it might not be very significant unless you put beside each other and look closely to compare.
Anyway, tempered glass is supposed to absorb any impact on the screen when dropped, thus having a film inbetween might affect this too. (My own feel)
So I think it is still better to tear off the factory film and paste the TGSP over the naked screen. I have been doing this and so far non of my phone's screen crack when dropped. *touch wood*