There is another option...
Now that we can have a lot of different railtypes in a game, you can make a couple of railtypes that only have a difference in tunnel entrances.
Full tile tunnels would do the trick in this case. And you can have different designs on top (grass, concrete, other eyecandy like houses/flowerbeds/etc).
I am (very slowly though, so patience ) working on a railtype set that has a couple of fulltile tunnels. Also with rails that have fulltile concrete/grass rather than catenary wires, that will fix this issue:
Also switches and signals will be covered up that way.
The difference for me will be that I will allow all trains to use those tracks, I know of one trackset that has some parts described above, but that is for 3rd rail (metro) only.
But, as I said, I am very slowly working on this.