It might be a good idea to add a few tiers of train research that boost hp of trains. Wagons and locomotives both. I've noticed as the game scales up the biters end up able to damage even nuclear trains badly enough to kill one car even when they pass at full speed. This causes the entire train to stop, causing a blockage, stopping more trains, which then get attacked by biters, etc...

Alternatively perhaps some sort of equipment that increases hp like armor? That would be interesting and have effects on lots of different things, trading space for hp maximum. I'm aware that quality does boost hp as well, of course, but having more options to protect trains as they go would be helpful.

Another interesting option would be a high-capacity low-regen shield which might specifically be suited for such situations, that has a lot of the traits of armor without needing some special system.

Unfortunately, only characters can equip armor. There are no ways to increase the resistances or health of other objects.
This is a great shame, as it was the easiest way to create rare but more powerful enemy squads.

As for energy shields, the existing shield in RA is quite powerful

Regarding the situation where the biters can stop the train, I believe it's due to one-shot protection.
Someday I need to add the "impact" damage type to the exceptions.

I shouldn't expect this in the foreseeable future, because finalizing the RA/Rampant fixed mods took too much effort and now I don't want to do anything else