Vertical biome overlap may be an intentional feature, but there's a side effect that's been causing an issue for me.

In previous versions, I've built my home on a mushroom island. I can use the "Biome:" tag in the F3 menu to help extend the terrain to the very edges of the biome without building into the ocean.

However, in newer versions, there have been hostile mobs spawning on the edges of these mushroom islands. The blocks they're spawning on are within the "Biome: minecraft:mushroom_field_shore" boundaries, but they still continue to spawn, and I believe it's because the blocks above the mushroom field shore are ocean.

I think this is a symptom of Minecraft 1.16's vertical nether biomes.