Well the phone uses a special glass developed for flexibility. And there are 96 force sensors in the added layer below backlight. The watch is one sensor for entire face I believe. If the movie Apple put out showing how 3D touch works is to be believed, the screen glass shows specific deflection, bending of glass at the localized position of the finger push. My concern is that a glass screen cover would mitigate, mute, or spread out this deflection.It doesn't on the watch, so there's no reason that it would on the phone.
I like using the Zagg glass so I am hoping it can still be used with the 3D Touch screen, but I need to see it tried before I would chance it. What worries me is that Apple along with Corning needed to come up with this flexible glass. Means that current glass was too rigid to register properly.
The whole system appears to be rather complex as it utilizes the accelerometer as well to determine if gravity needs to be added or subtracted based on position of phone and any phone movement at time of touch. Molecular distances are being measured here. Space between bottom of glass and sensors below backlight are tiny.
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