The reason i can think of would be having every circuit in line so an argument regarding what Pit Entrances can be exploited to advantage does not occur. Of course not every Pit Entrance can be used to an advantage, however if we could completely skip the debate about which ones are and which are not, that's a positive.
As for Pit Exits, i suppose this has more to do with not having a monster incident on the Pit Straight; like you said. It's not just with unsafe pit exit's though, Nobody is perfect when seeing where cars around us are, and there is the possibility of a driver thinking he is clear from the Pit Exit, theres no advantage to cutting the line, so he moves over early across the White Line, buuuuuuut he has now had a huge accident as there was a car just out of his line of sight when he checked. I'll provide an 'Extreme' real life example below.
I totally understand where you're coming from with 'There needs to be a reason for a rule' and 'Not having a rule for the sake of rules' as i agree with you. However i do see the logic for this rule. Saves thread debates and if we enforce it at every single round, every single circuit, then this is the last we'll ever hear of it i'm sure.
Let's pretend that Rubens was not forced over the white line, but just alongside it and that there is a car coming out of the Pitlane. He thinks he is clear, there is no penalty for crossing the Pit Exit line so he begins to rejoin the Racing Line.
By not having this ruling on every circuit for the simple fact of 'It does not provide an advantage', if somebody is not following Pit Exit procedure and they wander onto the track because they 'Thought' it was clear, they have now just caused a monumental crash, one car has his race ruined through no fault of his own and the other has been pile drove from behind due to not staying with the set boundaries.