okay...
First, it is incorrect to think that having more than one build option adds appreciably to the cost in an optimized manufacturing process. A common platform with different build substitution lists and multiple part streams that is planned out in advance mitigates this fictional "increased cost of multiple options." A door is a door, and whether you stick electromechanical or manual actuators in it doesn't create a large labor difference to trained floor personnel.
For example, we offer a product that comes in different flavors. It consists of an electronic board, housing, connectors, and so on. There are three circuit boards in the product. Between all of the flavors, the circuit boards are exactly the same, and the only thing we change is which components get installed on the circuit board.
In a vehicle, the door is the door. The only thing that changes is whether the electrical 'stuff' gets installed, or the manual 'stuff'. The cost differential is in the components that are installed.
For a crank and linkage, you're probably talking about $3-4 in component cost. For an electric motor, that has a 7 year expected product lifetime, an automotive environmental rating (-40C to +125C), current and thermal limiting, transient protection, and safety logic in the case of the auto-up, the component cost is at least an order of magnitude larger. The installation time is not significantly different between the two with both component streams available at the point-of-installation.
The electrical components also have many more defect opportunities than the manual components, tracing all the way from the fuse to the switch to the motor. There are more warranty claims for an electric setup than for the manual setup, and the warranty claims will similarly be an order of magnitude larger for the power windows. Longer MTTR and shorter MTTF are the key issues here. Longer MTTR (Mean time to repair) means more time is spent diagnosing an issue, locating the defective component, and replacing it. In a manual setup, an issue is limited to something in the door. In a power setup, it could be anywhere from the battery to the door or anywhere in between. Shorter MTTF (mean time to failure) means the electric components fail more frequently and after a shorter time than the manual ones.
Now, let's take all of those people who want manual windows and tell them we don't offer them. They don't want to, and aren't going to pay for them. We're going to have to do one of two things: give them the power windows for free, encumbering ourselves with the past, present, and future burdened costs of them (past sunk cost on the balance sheet for setting up the process, present cost of components, and future cost of warranty claims), or, we won't sell the car, meaning an opportunity cost of whatever the profit is on the vehicle, or at the very least the dealer-incurred floorplanning cost and the time-value of money for the manufacturer that is incurred by selling the car later.
I could be a lot more detailed, but this isn't what I wanted to be doing on my vacation

But, I hope this gives you an idea that there's a lot more that goes into it than just considering the complexity of multiple component streams (which doesn't even really add much to the cost).