Hi,
The Edge Boundary Checking mode is not meant to "slice" the geometry, it's removing elements within one item that are "based out of area used for distribution" - t used object(s) should be "divided into Elements". If there are any "overhanging faces" under one element, these will be fully removed or not, depending on whether the element is based inside/outside of the distribution area.
You might consider using our RailClone plug-in, which allows slicing the geometry.
I hope that helps.
Best regards,