No, screen protectors won't break 3D Touch on iPhone 6s/6s Plus
After some digging, we got a hold of the lengthy manual referred to in Schiller's e-mail, and can confirm that even though it has been updated to include detailed schematics and instructions on creating for the iPhone 6s and 6s Plus, the requirements for screen covers haven't changed. Indeed, so long as manufacturers check the following three boxes, their screen guards will not interfere with the workings of 3D Touch:
If a case design requires the Apple device's touchscreen to be covered with an overlay, the overlay must not:
● exceed 0.3 mm in thickness
● introduce air gaps between the touchscreen and overlay
● be electrically conductive
● exceed 0.3 mm in thickness
● introduce air gaps between the touchscreen and overlay
● be electrically conductive
In other words, don't worry about ordering a protector in advance of your new iPhone. It will more than likely work fine with 3D Touch.
source: 3D Techtronics
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Things that are NOT allowed: