Apple wants a certain profit margin for the model as a whole. Yet for customers who will never pay prices that will give Apple that full margin, they offer a model at a low price point with a compressed margin, but with a painful aspect that will encourage customers who can pay to go with a higher priced unit — here, the painful thing is the small SSD size.
So the idea that the minimal-SSD model is somehow the "real" price and Apple is selling SSD space at an exorbitant markup, isn't quite right.
You could almost think of it as Apple offering a discount if you'll go with the smallest SSD, so they can capture more of the market while still keeping their average profit margins high.
If Apple charged "competitive $/TB prices", the small-SSD option would likely be more expensive, rather than the larger-SSD options being cheaper.