Hi, as expected the factorio forums thread was moved to "not a bug." Here's what posila wrote.
Thanks for the report.
This is not a bug in the base game.
It is either issue with the mod, or maybe the mod even intended this behavior.
If it is not intended behavior, the mod should set rail collision mask to collide with "floor-layer" or "object-layer" or both. (Vanilla rail collision mask is { "object-layer", "item-layer", "floor-layer", "water-tile" })
Here's the thread location now - https://forums.factorio.com/viewtopic.php?f=23&t=70766