In high-cost-of-living areas, there are two other major costs worth considering. First is the cost of daycare (or equivalently the opportunity cost of having a stay-at-home parent). My wife watches our son, and we're glad that she can afford to do that, but that's $100k of forgone take-home pay we're leaving on the table.

Second is the increased rent/mortgage of a house with an extra bedroom. I pay ~$600/mo more for an extra bedroom and have a substantially longer commute than most of my coworkers to live in a place that can accommodate our family.

Both of those costs far exceed anything else we've spent on our son, which mostly falls into the "optional" category you mentioned.

Both of these factors are much more important in high-cost-of-living areas, which may explain in part why there aren't many kids in San Francisco.