Generic - its try detect PAIR from photos and match "stereo" results say image 1 and 2, then image 3 and 4.....
Disabled - its try pair all images, say image one is aligned with all 99 images
For GIS application is with enough overlap best if use Generic Pairs ( but when have GPS info and GCPs then GROUND Control is better ) for things like statues and other complicated stuff is the Disabled pairs better.... depend on project, but when dealing a lot ( 100-200+ ) of images its faster to use image pairs....