TL;DR: That map is broken in all versions (steam and non-Steam) of the game and is likely to remain so.
It may be that you misinterpreted the referenced thread. The Original Poster (OP) - Captain Ford, asked for permission to upload a fixed map. That permission never came - even if it did come, the upload will happen to Colonial Space, since Alpha Sector was a showcase of maps made during game development and will not undergo further changes.
ThePenguin several times offered to fix the issues with Troublesome Trains 02, but never did so.
So, as it stands, that map is just a relic of ancient players having played and moved on
If you or anyone wishes to fix the CRPL code and upload the map to Colonial Space, you do not need to ask for permission.