For random world generation like this, how do you make changes to the generator (like adding taller mountains) without breaking saved games and world seeds that people have written down?

Guessing you could let the saved game or the player pick which world generation algorithm to use and you need to keep the code for the old and new generator around? It's probably less of a big deal for e.g. rouge-like games are over for good in a few hours, but not for games like Minecraft.