Adding a fingerprint scanner doesn't affect every component in the phone. It doesn't affect the display, CPU, dimensions or anything with a long lead time. It affects the power button. Apple had well enough time to add it.
I would give them some benefit of the doubt to one of the biggest companies in the world that they had at least a dozen people research this and came to the conclusion that they couldn’t or didn’t want to (due to cost, design, etc).
The same reason that Apple shipped broken keyboards with MacBooks for years. Because Tim Cook is not a product person. He is an operations person. Adding a fingerprint sensor is good for the product but bad for operations. Who do you think he's going to side with?
At the risk of using a cliche, I think Jobs would have made a different decision.
The answer seems obvious: they are pigheadedly stubborn when it comes to design decisions. They will never throw away a design decision within 5 years because that would be admitting they made a sub-optimal decision at some point. It simply is not on brand.