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Sometimes the loser feels too underconfident to initiate a GG, perhaps the winner takes it. It is not an egotistical thing, it should come off as humble in contrast to "lol go back 2 LoL you scrub shits". The winner would also be feeling happy with this game in this situation and it's in some ways a means of saying "thank the lord/people on my team/gaben for the game we have played today". Some say it out of habit, perhaps from playing Starcraft. Going without a GG at the end of a game in Starcraft is like picking up a woman and removing her from your house without saying any words, immediately after sex.
I do make sure not to say GG WP if the game of dota was by all means terrible, because to me it does somewhat deface the meaning it still has. If I went a normal score and didn't get to stomp and had no fun, but all of the other team went really shit anyway and it pretty much was a stomp, then it was not a GG (I didn't get to stomp and the game was not close and intense) and it was not WP (the other team sucked).