The notion that a custom home is more expensive than a finished, unsold home ("spec home") perhaps comes from the fact that in a custom scenario, you have a nearly full-spectrum menu of options. It can be tempting to add more amenities because you have the opportunity to do so.
But I do not price custom homes higher than spec homes. Both types of homes have a base price for the plan (which may or may not include cost considerations for any deviations from the original plan), and the cost of the lot. Beyond those two components, you as the client have essential control in the pricing based on what amenities you want above and beyond my signature amenities.
A spec home will almost always include additional amenities that I've chosen to implement, either because they are commonly-sought amenities or just ones I felt compelled to implement in this home. Those amenities may not have been ones you would have chosen if given the chance in a custom scenario, but they are still priced in. So in this situation, you'd be paying for amenities you wouldn't have otherwise chosen and thus the cost is potentially higher than if it had been a customized build without those amenities.
One other factor that can come into play is that, while my spec homes most often sell before they are complete, there are times when a home is completed and sits on the market waiting for its buyer to discover it. I may choose to discount this home to help incentivize its sale depending on how long it has been on the market, or where we are in the given seasonal sales cycle. In this case, custom building an identical home would have a higher price than the completed spec available for purchase.