Watching Ken Burn's Civil War Documentary one of the segments is called Bottom Rail On Top. The name is inspired by a story involving a Union Soldier who was once a slave. The man sees his old master, now a captured Confederate prisoner. The Union Soldier went to his former master and said, "Howdy Massa. Bottom rail on top, this time."
It's understood that the phrase is an idiom that means, as Wiki writes, "to reverse a hierarchy." I get that that's what it means as an idiom, but I am interested in what may have inspired the idiom to have that meaning. Perhaps there is a railroad mechanic that has the function of taking a rail and subordinating it to another or something.
Of course it is completely likely I'm over thinking this.
If you are thinking that the expression has anything to do with the railroad then yes, you are overthinking it.
The expression refers to fencing, that is the post and rail fencing that was normal in rural areas before the invention and popularization of barbed wire. It involves vertical wooden posts connected by horizontal wooden rails. Depending on the height of the fence there would be at least two, and possibly three levels of horizontal rails. These fences required regular maintenance and repair. The rails between any two posts would necessarily be of the same length and hence interchangeable. So if the bottom rail is on top this time then the top rail has been moved lower down..