Would it be possible to have variations of the locomotive for each fuel type, so it scales to the endgame rather than falling short of the benefit of carrying a train and nuclear fuel?

I cannot use the fuel-modifier (because the equipment uses no fuel) and it is not possible to create new bonuses to boost the equipment.
But I could add a new research for a "Nuclear Railway Motor Car" which is faster (and uses more power). But I would not add intermediate versions with only minor speed boosts.

Do you have specific mods in mind, or just the vanilla game (possibly with unrelated mods)?

The vanilla game's acceleration and speed bonus from nuclear fuel would be sufficient with the mods I use leaving their fuel properties alone.

Integration with the Spidertron-to-train behavior of https://mods.factorio.com/mod/SpidertronEnhancements would be nice if you can manage something with that. I haven't tested to see if the two mods can work together, yet.

Just added a new technology + equipment with 0.1.4.

My mod has no issues with SpidertronEnhancements but I cannot imagine a way for both to interact. My mod uses the default "enter"-button to enter and exit the motor car (unlike that mod, which uses the "U"-button). Meaning it would be impossible to exit the spidertron while standing on the railway (because the player jumps from the spidertron to the motorcar).
And I don't want to create bugs by swapping out the rides (it may be possible that the spidertron disappears and equipment is destroyed).