If you're setting the front end of the amp to do most of your distortion, it will also compress. Some people like the EQ pedal before that compression and distortion happen. Some don't want that, and want to have the EQ see the "finished" preamp signal before it hits the power tubes.
Both ways definitely have their own thing happening, and there really aren't any rules for which is better - it's up to the player, and sometimes, depends on the situation and the particular song.