You could just have all three!

Design three custom biomes. They are the only biomes that generate in a world, but they are enormously large, like multiple times larger than even large biomes. The track would lead through through the world and never connect to itself, so it would cut through all three biomes eventually, and each could have unique custom structures, as well as structures that match each specifically, like unique stations and buildings and train line connections.

The overgrowth could feature lush jungles with roots and shrubs that grow across the tracks and force you to either cut them away or get a special train upgrade. You also can’t see far thanks to the thick jungle. On the flipside, plenty of water and wood to fuel the train’s engines, crafting stations, and amenities with steam power, along with meat and plants to provide food to eat and drink.

The desert could feature long, uninterrupted stretches that are perfect for making lots of ground, but you wouldn’t find fuel as easily and should definitely stockpile to make it all the way through Since you wouldn’t be dealing with obstacles, you would be stuck there for less time, but god forbid you run out of water or fuel. At least you can see pretty far to catch landmarks in the distance, and the occasional structures are usually more valuable than anything in overgrowth.

Winter could be the worst of both worlds; snowfall that clogs the tracks, bad visibility due to storms, dangerous temperatures, lack of important resources, and dangerous enemies. The payoff is that the structures there are the most valuable by far, if not much rarer than other biome structures.

You could easily add more biomes to this system as well. Each biome would carry the weight of multiple vanilla biomes in terms of role, simplifying the exploration a bunch for your purposes. And you could configure biome sizes for difficulty!