I wouldn't lump all trains in the category of having holding tanks. At least until the early '90s, Amtrak trains didn't, and you were requested to not use the on board toilets at the stations. Some (maybe all, I'm not sure) Amtrak trains got tanks starting in the early to mid '90s. Before that I remember reading the occasional cautionary tale in the newspaper about fishing under railroad bridges when somebody reported learning the hard way. I'm pretty sure that in much of the less developed world, direct track dumping is still common.