The costs on such components is pennies, and Apple honestly isn’t shy about just charging more to cover their costs.
I do honestly believe they made those decisions to cut down on total space. The headphone jack alone is gigantic, and the home button required an entire bar of potential screen real estate dedicated to it.
Were there other options? Sure. They could have had the home button under the screen or something, but honestly their decision was likely the best choice. Which is only furthered by the fact that virtually everyone is doing the same thing now.
That said, moving from physical buttons to solid state buttons with haptic feedback… I don’t see how that could cost less. Honestly if it cost less, others would likely already be taking that shortcut.
I’d wager it costs a little more per phone, and they will charge an extra $100 for that “premium” feature. Simply because they can.