When using BiomeGrid#setBiome(int, int, int, Biome), or the (deprecated) BiomeGrid#setBiome(int, int, Biome) within ChunkGenerator#generateChunkData, the area in which the biome is set is populated (via Vanilla populators) as if the Biome was never changed.

The biome change itself is not the issue, as it can be detected during custom population, as well as things such as grass color and mob spawning reflecting the correct biome, as well as the correct ID being shown in the F3 menu showing that the change is recognized by both server and client.

In theory, since chunk generation occurs before population, biome changes there should affect what is populated in the modified area.

For example: setting the biome of a large area to end_highlands should prevent the generation of small End Islands (the small circular ones), as they only generate in the small_end_islands biome. However, even after the biome is changed during generation, they still generate in the areas that were previously small_end_islands.

Note that this functions as expected in Paper 1.15 (But not in Paper 1.16)