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).
At the risk of using a cliche, I think Jobs would have made a different decision.
This is far easier on an iPad which has that design decision made up front.