If tunnel entrances are enough distant I don't know why crossing tunnels should be forbidden, if they don't make your trains exit the tunnel from a wrong exit (try to build a tunnel 'inside' another with the same method you used, if you can) I think they might be allowed, but the entrance must be at least 2-3 tiles away from the intersection (so parallel tunnels should be forbidden)
This is what I mean (side view)
IMO this might open the path to other nice junctions etc, and if we might get crossing bridges too it should be the same thing, with the top bridge longer than the bottom bridge
We already have crossing tunnels in trunk since long time; only thing is that it's considered a cheat option. This patch should definately not change this, if the author wants to have any chance for trunk inclusion.
The point is (what I reported above and hackalittlebit already fixed) that it was possible with some dirty tricks abusing this patch for making crossing tunnels without
having activated the crossing tunnels cheat.
If you'd like to have crossing tunnels available in multiplayer (i.e. changing it from a cheat to an advanced setting), this would be a thing for a seperate patch. Keep in mind though that it was decided to make this a cheat for a reason - it's totally unexplainable how you can have two really short tunnels crossing. So just moving it from cheats to advanced settings won't do the trick - you'd have to implement something to make sure the entrances of the tunnels are sufficiently far from each other.
Wouldn't this be a topic for a patch by you, wolf?
edit: just now read your post, hackalittlebit, answering in a minute