In short, you want an option to let players set how far away the train should be behind the train ahead?
I personally disagree on allowing the players to choose, for the following points.
One point is by having a delay, the game can let the player know they need to "re-organize" the line's layout, or to "re-optimize" their lines around, as a method of feedback. Meaning, this is how the game directly tells the player, "we can continue to let trains run on this line, but it would be nice if you could do something about it. Or we can just continue the way it is."
The other point is, realistically, trains should wait in subsequent stations behind the first train letting the passengers on board. For example, in Boston, when there are rush hours, the metro trains on the Orange Line would cramp together , and stays put away from the train in front. That way, passengers at the overcrowded stations (Downtown Crossing) will be able to aboard trains quickly as each train runs by in succession.
Problem is, also realistically, the Metro/Regional Transit Authority (or the public transit authority, in general) cannot predict and control how often a train should come/go to those stations when rush hours occur. That is what your "automatic wait delay" does in the game, where it is simulated to have the effect where the train behind the leading train must wait for the train to pass.
But, for the benefit of the doubt, tell us what your opinion is about this "automatic wait delay"? Once we know of your opinion, the developers will be able to read them and consider what you feel about it.