I'm just going to leave this quote here:
'If you keep your eye on the profit, you’re going to skimp on the product. But if you focus on making really great products, then the profits will follow.'
Changing the base storage may impact Apple's profits. It may not. I don't know, I don't have access to their account and margins and user statistics to find out.
What I do know is that, in this day and age, 16GB is skimping on the product for the sake of the bottom line. That's not the ideology which got Apple where it is today. Sure, they made products which were very profitable, but by and large you could buy any product and the experience would be fantastic. Buying a 16GB iPhone now means you're going to have to consider turning off 4K recording and Live Photos, not downloading software updates over the air and avoiding new games which can have a very large file size.
That's not a fantastic experience.