I'm about to do the Prescott boss battle in episode 2 but I haven't repaired the train station in Bog Easy yet because the train conductor never initiated the TV watching dialogue so I could never bring him to his station. If I beat the Prescott boss, will it be too late to save the train station or will it be destroyed?
No, it isn't too late. You could not do it before you opened the wall in Bog Easy Old Town and entered the projector screen to Blot Alley. You could have turned around and gone back through the screen to do some Bog Easy Projects. It is following the game path that you proceeded to this Boss Fight, and will be returned to Mean Street, to do chores, like going to Bog Easy.
At first, the train manager was outside the store door. Even after you got rid of the Beetleworx, he would not come over to the dock. He would never come to the dock until you went through the projector screen to Blot Alley.
So, when you come back, look him up, and cajole him ...
When you deal with him, and want more, let us know.
WARNING: Earthquakes are happening, and if you do not repair, activate, and open the train stations -- and report back to the Station Master in Mean Street South -- the stations could be irreparable damaged, and boarded up, with no conductor in them or around them.