When a train passes the same coordinate that the player is - the player gets teleported. Even thought the player and the train was on different planets... Or something like that happens all the time...

I'm afraid I can't reproduce this. I tried with a train going round a track on Nauvis, then travelled to the same coords on Gleba and it worked fine. I also tried putting down rails on Gleba in the same position as Nauvis, and also switched to the Preemptive and the Reactive Only options and couldn't see any problems.
Can you give more information?

This happens when, in viewing mode, the center of the screen, where the player himself should be, coincides with the place where the train is moving.
A reasonable solution that can be made is to move the player from the railroad tracks to a safe place and turn off the protection function before entering viewing mode. And when returning to control the player, turn on the protection function.
The second option is to not react to the center point of the screen (where the player should be) in viewing mode.

+1 to this issue - I just got "run over" by a cargo ship while in map/remote view and this mod teleported me to Fulgora.