So, find the parts that OnePlus put in the One and show the cost that they paid for those parts.
OnePlus One with 16GB NAND: $300
OnePlus One with 64GB NAND: $350
Run the cost of NAND chips. 64GB MLC NAND chips fluctuate at a spot price between $1.60 and $4.34. Adding 64GB of NAND to a platform costs $4.34, much less switching from an expensive 16GB NAND platform to a 64GB platform. A 32GB chip fluctuates between $1.70 and $2.93--two of those would cost $3.40 to $5.86--and the next common size down is 4GB MLC NAND. Once the manufacture process is reliable, the sheer silicon wafer size is what counts: a wafer carrying 32GB of NAND costs exactly as much as a wafer carrying 64GB NAND if exactly half of the 64GB NAND chips are non-functional due to manufacture errors and 100% of the 32GB NAND wafers are in working order.
Of course bulk agreements mean we can slim profit margins down: if I were to buy a million chips from a supplier, that supplier would make a large order from his silicon supplier, who would make a large order from his material supplier, who would make a large order from fuel and energy suppliers, and so forth. Each could negotiate a large purchase contract by which a sizable profit is made on large volume and slim margin, at each step compounding the per-unit cost savings in the final product, delivering to me at substantially below-market price.
I don't pretend to know that OnePlus paid $4 or $1.60 or so per 64GB chip; I am fully aware they likely paid substantially below-market, and that the market price I cite assumes they went fully off-the-shelf for small batches (which may have happened) and so paid more than they otherwise would have. I can't very well conjecture about how much less they might have paid than the amount I cite; I've had to run this based on the most expensive component prices available on the market.
Ask them what their profit margins are on both models, and ask them why the bigger one is $50 more.
The profit margin is demonstrably larger on the one with bigger NAND. You can ask them, but things like profit margins in specific are strategic business information: advertising that you're gouging people for additional luxury is a good way to destroy consumer faith by arrogance and entitlement, and of course lead competitors to create a strategic opportunity by advertising that they don't gouge quite so hard when add extra NAND (the opportunity is to discredit your operations and to capture your market).
Small business or not, you'd be a fool to be that transparent.