Think about it the other way around: Apple could easily afford to put the
largest amount of storage they offer in
all their phones. From their perspective, it wouldn't be much of a cost difference in the BOM.
But, if they only had the one phone model, how would they decide what to charge for it?
If they charge a lower price, everyone buys the phone, but they're leaving money on the table because they know that some people would have paid more.
If they charge a higher price, some people don't buy the phone, and again, they leave money on the table, because their margin is large enough that they still could have made a reasonable profit off of these people selling them the same phone.
Price discrimination—a.k.a price discovery—is a way of taking one product, and selling it for two (or more) separate prices, by having people self-select into your lower or higher price "tiers" based on some feature that costs you essentially nothing—a feature which you probably could offer everybody, even for the base price—but which you intentionally remove from lower pricing tiers, so that only the people who value "a low price" more than that feature will select into that tier.
So, for Apple, price discrimination is them ordering NAND of smaller sizes—even though this isn't really saving them money, because it's bloating their manufacturing logistics matrix—just in order to make the experience of using their entry-level phone models worse, in such a way that they can specifically target price-sensitive customers with those worse phones. Then they can crank up the price for everyone else, because now they don't have to worry about scaring the price-sensitive away: they've already made a low-tier crippled offering to serve them.