The space trains cannot use the "Vehicle Fuel" fuel category that Krastorio 2 introduces. The mod also removes the acceleration bonus from vanilla fuels and introduces a penalty to most of them. Because the trains are so fast it isn't really a problem but it feels out of place to refuel them using "less processed" fuels.
I'm not the most knowledgeable about modding so take this with a grain of salt but in my save the normal trains can use the normal fuel and the vehicle fuel and I'm pretty sure I've seen other entities capable of taking multiple types of fuel in other mods.