I think I understand what you are looking at - the stops are probably in a nice T slot in the front edge of the table, like most mill - drills. It makes a nice place to mount the scale for the x axis, but you have to remove the stops to do it, eliminating the ability to set stops. To answer you question of what are they used for? Well, they can be useful for anything that requires returning the x axis to the same point repeatedly. You might be milling a large pocket and set a stop just shy of each end of the x dimension and just have to watch the y and z, making sure each x axis pass starts and ends at the same point to rough in the dimension, removing the stops for the final clean up passes. Does that give you some idea? I'm sure someone with more experience than me can give more and better examples.
Dan