The 'missing' crossings are all DLS content.
The portals are hardly 'right in the middle' of the route - they are within a board or two of the end of the route so that as you approach them you don't see the end of the world approaching. If not having them at the edge of the world is an issue, lop off a board or two!
The HP houses are background content. All of my routes are designed to be viewed primarily from the trackside cameras, or from the cab. Anything that isn't trackside is as lo-poly and as quick to place as possible. Again if they offend, feel free to spend as much time as you like changing things around....