I have used the map object hider mod Map Objects Hider | ModHub | Farming Simulator (farming-simulator.com) by Achimobil to remove sections of in game track, then use my track to tie into it and that worked pretty well! Just stay clear of the in game train when it comes through...
Viewing post in Placeable Railroad Track comments
If you go into the map that you are wanting to play and look in the xml files for the trainSystem.xml and just rename it to trainSystem_old.xml the game wont recognize it and the in game train wont run - but you still will get the in game train sounds so it sounds like a distant train is running and you wont have an in game train to worry about hitting you