Off the top of my head:
- Tubing is sourced from a more expensive source, or made in a more expensive market
- Butted tubing
- Shaped or heavily worked tubes
- Custom-drawn tubes
- Dropouts, bottom brackets, head tubes are unique to the brand instead of purchased off the shelf, and/or options are offered
- Finishing work options
- employee wages higher in some markets, and in-demand skills warrant higher wages
- Employers who pay an overall better wage, and/or offer healthcare
- Finishing quality, finishing options.
- Marketing, including racing programs
- brand value
Of that list, only the last one doesn't have a directly measurable cost associated with it, although it's generally an output of all the points above it.