(Note: Grade Separation in quotes because it's not necessarily actual grade separation - just the illusion of such)
When watching the train launch pads, it came to mind that although Factorio was patched to fix the workaround that allowed for https://mods.factorio.com/mod/rail-bridge to work, the way Renai works could actually be 'adapted' (haven't read the source code; am unsure of the feasibility) to support actual railway bridges (or at least the illusion of such). Although I have not tried out the mod myself, my understanding is that as long as there is a launch pad and a track at the landing site, the mod allows for trains to pass in a grade separated manner (albeit currently with one train flying over the other).
It therefore came to mind that if you could force start and end points for the flying, all you'd need are placeholder graphics for the 'bridge' (and adjustment of the train graphics in midair) and we'd suddenly have actual train bridges. Of course mod compatibility would be a wreck and there would be a lot of edge cases, but if used for the specific purpose, it might actually provide a vanilla-ish method for grade separating train lines.
Just a thought; will definitely try out this mod on my next Factorio map regardless since it seems like a lot of fun.