MC-42819 removes blaze spawners, which makes it impossible to beat the game, because there is no longer a way to get eyes of ender. The addition of villages makes it desirable for some players to turn off generated structures to make the gameplay more difficult. You could potentially save zombie villagers if blaze rods were still attainable somehow.

The inclusion of underground railways like the one at -45 : 21 : 27 (seed 1) clearly doesn't comply the remove-generated-structures rule, another feature that could potentially make game-play harder if removed and enhance gameplay for "hardcore" players.

The main issue is that "generate structures" is a nice feature to have if it does not make gameplay impossible.