From what I understand of the process (and this is purely from all the information provided at the Keynote so forgive me): they bombard the glass screen with positively charged ions in a super collider. The glass then travels through space-time, becoming stronger and stronger each trip because of the inherent stresses of time travel. After 143 years (equivalent, remember this all happens in an instant, it's very technical), the glass arrives situated perfectly atop the completed iPhone on the assembly line.
Then you get one, sit on it (or drop it), shatter the screen, and can still blame Apple anyway.
Turns out, even with ion strengthening, GLASS IS GLASS.