You should check out the program called tracker-config. It not only lets you set all these parameters manually (thus making tracker actually, y'know, bearable), but it also helps on understanding how it works.
Tracker is all open source, so you can check out exactly what's being done from the code (the manual pages are the best place to start). According to the trackerd manual page, all three groups automatically include all (non-hidden) subdirectories.