When merging two or more route together it is better to add a board or two in between the routes. These boards can then be sceniced to smoothly blend the terrain together on the two routes. The number of boards to be added will depend on how much effort you are prepared to put into them and also on the height difference (if any) between the two routes. If the height difference is considerable then it will require more intermediate boards to keep the gradient at a reasonable rate.
You could place 2 backgrounds on each route to block the view of the other unsightly route, and Portal trains to, and from, and hide the 2 Portals in a forest of trees, or place a tunnel portal spline, or building asset, over top of the Portal