Are there other elements of the manufacturing process that creates a better constructed house than traditional site-built homes?

Yes. The engineering design and controls are key elements to the manufacturing process that are not available on a traditionally built home job site. The finished house from a quality manufacturer should have straighter walls and ceilings with less potential for visible signs of settling.

Straighter walls with less likelihood to be affected by settling should also mean better functioning doors as your foundation settles. Certain manufacturers use a hi-tech method of securing the drywall to the studs to improve performance which minimizes settling nail pops. A quality manufacturer will employ a third party engineering firm to provide quality control checks throughout the manufacturing process.

Self-supporting ready-made components are used, so the need for formwork, shuttering and scaffolding is greatly reduced.
Construction time is reduced and buildings are completed sooner, allowing an earlier return of the capital invested.
On-site construction and congestion is minimized.
Quality control can be easier in a factory assembly line setting than a construction site setting.
Prefabrication can be located where skilled labour is more readily available and costs of labour, power, materials, space and overheads are lower.
Time spent in bad weather or hazardous environments at the construction site is minimized.
Less waste may occur
Advanced materials such as sandwich-structured composite can be easily used, improving thermal and sound insulation and airtightness
For more :http://en.wikipedia.org/wiki/Prefabrication

The buildings are earthquake resistant. It is made by scientific methods and vastu shastra. The quality of building is also good. It has good longevity.

Construction is of various type. It depend on your engineer. He can propose better constructing idea each time.