Depending on your production quality, the PPM values for the production line defined in the Options.

You can Modify the default values or set specific defect values for each Package Group e.g. your Chip values better like QFN soldering then change the PPM value for one Package Group. This values modify the Porduction Yield directly and the Test Efficiency in small parts (see calculations above).
With the option "Calculate values regardless of the capabilities of the machines" the percent values has the same basis (real PCB data) or use the machine results for calculation (e.g. only checked components of the analysis result like count BGA + QFNs in AXI analysis).