Apple has huge margins, it's not a problem unless you think about margins. Making more money is normally good, even if the margin is slightly lower.
More skus is really really expensive quite often. You can end up with a low run product that is even more expensive than a 'premium' larger/nicer product.
If the margin is lower then you make less money not more.
But it’s better to sell phones with better margin. More people need to take Econ 101. Opportunity cost is an actual thing. You can be sure they did the math. Selling ever so slightly fewer larger phones at higher margin is better than selling slightly more phones at a lower margin.
Apple knows its sales and profits much better than anyone else.