Not running it in any mode at all. Just running it, same as I've always done.
I could try building the same system again, and see what happens. Another thought: I could try reducing the number of trains, and see if that reduction in load on the game engine solves the problem. That would be the easiest first test.
Edit: Had another idea for a quick and easy test. Simply remove some of the cross connections, to bring it back to a simpler track layout, then see if it still crashes. If it does, the glitch is something else. If it doesn't, then the number of cross connections would be the obvious cause.
Only catch with this test is that, if the game engine is already at its limits, the recalculations necessary when the track is simplified might cause CTD anyway. Have to try it and see what happens.
I think (guess) a large part of the issue is that with the level crossings being cross-connected in every possible way, within the space of very few map squares, the calculations for possible routing of 140 trains are frying the game engine, and it just breaks down sometimes. It's not a congestion problem as such (traffic flows rather well) and it's not the actual number of trains being excessive. It's checking the number of possible ways a particular train can reach a given destination, and figuring out the best option, and doing
that for all 140 trains. And it has to be done very fast, because the cross-connections are so close together.
I'm guessing this is the issue because this is the only game where I tried this amount of connections close together, and it is the only game where the "exploding stations syndrome" has appeared. It's a bummer because the traffic flow in the Sydney area is actually very good with this setup. The routing is very efficient (and it looks great too).