The problem is that for Apple, the risk of putting the Saphire into the phones without backup would be atronomical. You act like both had the same risk? The potential losses on Apple's side of not being able to get the 6+ , 6 out would be tens of billions of dollars of profits, plus if the screen is not up to snuff, big loss of reputation and further big loss of sales and profits.
The phone already are back ordered, so you can imagine that if GTAT couldn't even manage Apple's initial expectations, that they probably couldn't manage the current heightened expectations.
You are assuming that this was for iPhone displays. To the best of my knowledge that rumor has never been confirmed. In fact, Apple's intended use for the sapphire from GT has never been publicly confirmed.
Also, were the situation handled differently a couple of months ago, the situation now might also be different. But that we'll never know...