It absolutely is making fun of all sides. But in the same way Blazing Saddles made fun of all different kinds of Americans.
There is still very clearly a righteous protagonist and a nefarious antagonist. The nature of the story is absurd, but the message is crystal clear to anyway with half an ear listening.
I am absolutely a gamer but not as much as a capital-G Gamer like some of my friends are. Recommended DE to one, who is admittedly like a baby communist at best (imagine your average left-leaning poli sci major who graduated and realized 'oh, this is all basically about screwing over the average person' after their first job in DC & only then started actually reading theory and you've got him) but also an alcoholic so I was thinking he'd definitely get something out of this game if he plays it. Tried not to spoil any of it for him but since I know he is the type of person to literally watch playthroughs of games he hasn't played yet and spoil himself - I was like "if you do play it - try being a communist your first playthrough and finish the entire quest, the ending to it is my favorite part of the game"
Asked him how he thought it was like a week after he finished the game. Man literally did not get the message behind the tower. "I dunno why you like it, isn't it saying that communism is doomed to fail?"