I don't want to sound negative, but don't see how I can avoid it without sounding untruthful. Tunnels in Trainz are wildly unrealistic under any circumstances except, perhaps, straight-as-a-die track (how often does that occur in prototype in tunnel territory?), through absolutely no fault of the creators or the users, I wish to emphasize. Even if you lick the "snap to" business, the bore of the tunnel looks like it was laid out by an inebriated crew of grave diggers unless it is perfectly straight. It is almost impossible to lay out a reasonable track structure. The tunnel track itself, with the accompanying bore structure, just doesn't seem to follow the same rules as track laid on the surface. When you run a train through the tunnel the engine exhaust will seep through a hundred or so feet of dirt to the surface so you can follow it and track your train's progress by following the little tornados of smoke asphyxiating nearby surface dwellers in chase camera mode, while your train goes spelunking along. Most of the tunnel portals are forced, again through no fault of the creators, to resort to Stalinist architectural school monumental portals to cover up the rips in space-time that occur when a dig hole is placed.
My solution is a punt, or perhaps, a quick kick. I simply lay out the track in a prototypical way according to the track chart or diagram I am using, or whatever I have preplanned, then superimpose a suitable tunnel, but without connecting it to the track. I elevate the real track or lower the tunnel high or low enough to mask the tunnel track, and, voila, after setting the portals at an appropriate angle to the track there is a realistic track layout. The hillside that is within the tunnel portal itself can be worked a bit back to the rear, and then colored with an appropriate texture. I use the pure black HOG texture, HOG 69, I believe. This will not work if you are into sitting in the train in tunnels, of course.
There may be hope. TrainzItalia is ready to release their version of the Donner Pass route. This will include a raft of custom assets. Since this route features miles of tunnels and snowsheds, it is possible that many of these problems have been addressed. I am looking forward to it.
Bernie