Yes, it might be that the way was originaly designed to be placed as a second layer somehow?
For the Swedish trains, -2,0 should work in all directions (0,4 would only push the train in the lateral position, thus won't work for diagonal tracks), save that you might have to tweak it a little to fit the actual track graphic.
Regarding the rotations:
The n,s,se etc. defines in which direction you can EXIT the tile.
N= exit to the north only.
Nse= can exit to the north, south and east.
Ns= exit both north and south.