Occasionally, chunks that should reasonable have their blocks replaced with the specified replacement block simply spawn as completely unmodified chunks, block-wise.
An example can be found with the following seed and coordinates: 582983328860332295 and -362, 67, 69, with the following script:

Tweaker.setWorld("minecraft:overworld")

all_biomes = forAllBiomes()
all_biomes.registerGenBlockRep("minecraft:dirt", "minecraft:sandstone")
all_biomes.registerGenBlockRep("minecraft:grass_block", "minecraft:sandstone")
all_biomes.registerGenBlockRep("minecraft:stone", "minecraft:diamond_block")

A screenshot of the issue

I have not been able to find a reliable way of finding out which chunks break, but it is consistent when using the same seed and script.