1) Train separates when exiting the tunnel. I ran a train, with two engines facing opposite directions, in order to test.
They separated and one engine made it to destination, while one disappeared, when exiting tunnel. I entered the tunnel and it ran back out the opposite direction. I found it sitting on the tracks, a short distance from the entrance tunnel (roughly 10 track lengths).
2) I was running a 4 lane main line, 2 tracks going 2 directions. I tried to setup the tunnels so that the main line was going into the tunnels. Unfortunately, the tunnels got confused. I entered a tunnel, exited, immediately re-entered a tunnel, and exited on the parallel running track. It seems the hit box may be too big, and it caught the adjacent tunnel, forcing me back in and out the wrong tunnel. This forced me to go a different route, with the layout.
3) I found that if you set the condition, for the tunnel, to a time based with a 0 second delay, they do fairly well at movement. So there's that.
4) Is it possible to make a mod like this with bridges, as opposed to tunnels? I only ask because I would thing bridges would remove the need for treating it like stations, and would also remove the complications of working in the underground zone. I Doubt it's possible, but thought I'd throw it out there.
