I think that there should be an offset to the central rails.

I want to make use of the mod for a chunk aligned central rail, so an offset in either x or y might be a good idea to add, so that the rail can be centered in a chunk.

Have a play around with the EW lines (y-coord) or NS lines (x-coord) settings.

I did. It made a new set of lines with the offset, with original lines still in place.

The mod deliberately won't alter what it has already placed. I have a partial solution for this in the next version but it will still require some manual intervention (spoiler: it involves Chunk Explosives). I'm generally not happy with various mods randomly messing with worlds - the risk of massive damage is too high.

To see your experimental settings changes I usually recommend you jump in a train and go to the edge of the explored world. Then make changes as you see fit then explore further. For this reason I suggest using a throwaway world or copy of your main save.

I've beeing testing the entire thing by creating new worlds with the altered y or x coordinate settings.

And the x, y coords aren't working? I know that coords with oddvalues, eg 1,3 are currently dysfunctional due to rail alignment. I'll be enforcing only even-valued coords in next version 0.18.1

Well... Have a screenshot...

https://imgur.com/a/XQIt2z2

Try the newest version 0.18.1 of CR. I got a better result with that.

Interesting arrangement BTW. Most people use more than two rails per side rather than duplicate a line. But I can see some benefits when running lines off.

I did that mostly to show that I have two lines, rather than a single line moved to a different position.