Actually it costs about $5 more for Apple to put 32GB instead of 16Gb. Remember that we had 16Gb back in 2007/2008, price of SSD manufacturing has gone down exponentially to extremely low cost after 9 years. I'd gladly pay $655 instead of $650 for a 32gb flagship iphone, wouldn't you? And Apple wouldn't lose anything
Check out some teardown estimates:
iPhone SE manufacturing difference from 16GB to 64GB is $10, but Apple charges $100 more:
http://www.recode.net/2016/4/4/11585836/teardown-apples-iphone-se
In this estimate it says the difference in manufacturing cost between iPhone 6s 16GB and 64GB is $17:
http://www.ibtimes.com/iphone-6s-pl...ke-iphone-6-plus-ihs-teardown-reveals-2120667
Now, I know price teardown of Apple products don't include R&D costs and other factors, but we are talking about NAND (SSD) cost, a standard component.
One last thing, it's standard in the industry to ship 32GB devices nowadays, yet Apple stays stuck at 16GB. It's clear Apple is aiming at higher profit margins, beating record-high profits last year. Now, it's nice and cool for Apple to pursue record-high profits, but I think there should be a balance between milking the userbase to no end, and giving away a bit more than usual, and I think Apple is currently unbalanced, and I think the market is finally reacting to this.