Wow, the thing about getting out of the map into the null void is awesome, I can see it as an easter egg, a more polished null void (like intentional) that could happen after certain kilometers. Also about the kilometers, maybe there could be more reasons to "brake" or "go fast" than just advance into the game, it will be really hard to stick decisions into a linear setup, but for example there is stuff you can use at your advantage: more difficult as you progress in time (so enemies scale with time like risk of rain 2), that is: unique enemies for each time frame, with modifiers.
Enemies would be the hardest task as you need to consider how many dimensions you have to parameterize, a fact is that how many permutations on that dimension doesn't mean how many unique enemies, so you could make some sort of 5 dimensions for the enemies that makes sense to combine when applied to unique enemies (if you kill them too close they explode and damage your train, enemies that are invulnerable until you kill its minions, etc) those are stuff you can combine with unique enemies.
it can easily fit the "spam enemies" fest and chain reactions, but I think the "bleak" atmosphere is a nice touch.
So your progression system can be based mostly on shooting a lever to change the path gives a lot of intention into the game, but at the same time keeps it linear enough to feel constrained, but that doesn't mean you cannot brainstorm like for example one of the paths leads to a portal at some point, your idea has a lot of expressions to make it progressive, you start on a more "realistic" and wasteland set until you advance into the game, even adding stations to buy stuff.
About the idea of expanding your train, I think this one would be more fitting for a "barotrauma" style, which is having a set of different looking submarines in that case (here would be unique train combinations) each with it's advantages, for example one could be more tanky but slow, others more fast but cannot have a certain weapon (like heavy damage weapons) and how that do an effect on future decisions. Technically you can expand the weapons (like slots) but not the train itself.
Regarding Artstyle I was imagining while playing, a washed palette, sort of 3/4 perspective and not too clean (somewhat noisy), it would be sort of a factorio train for example:
Good luck on this game if you decide on expand it, I would've love to help you on the art direction but I'm just a pixel artist.