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.
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In both cases I've experienced, it was a server. I can vouch that the the first server was 100% vanilla, though. I haven't attempted to reproduce in singleplayer, so I don't have a seed.
Edit: I'll see what I can do to reproduce in singleplayer.
Because I'm unable to recreate this in vanilla singleplayer in my attempts, let me list what I know:
The first server I played on was created in 1.16.3 with no mods (I helped the host set it up a couple months ago, and they didn't even know what Bukkit was when I was talking about this ticket to them earlier). I played on the server initially with Optifine, then we both began using Forge with a minimap mod. The server was still unmodded. Port forwarding wasn't an option for the host, so they ran ngrok so that I could connect to the server. When I ran into this issue, I swapped to a strictly vanilla client, and still noticed the issue.
Today, I was playing on a 1.16.x server. I was able to connect with vanilla 1.16.5. The new server is running some form of modded server file (it has several special commands), but I don't think that takes away from the same issue occurring as on the first server.
In this screenshot (on the newer server), the biome at Y=55 is mushroom_field_shore:
[media]In this screenshot (taken at the same X and Z coordinates), the biome at Y=63 is lukewarm_ocean:
[media]Perhaps this is a caching issue, where the biomes are cached from when I discovered them while using Optifine? In my first instance, I was able to see the issue with a vanilla 1.16.3 client on a vanilla 1.16.3 server, then in the second instance I was able to see the issue with a vanilla 1.16.5 client on a lightly modded 1.16.x server. In both instances, I discovered the terrain with an Optifine client, but swapped to a vanilla client and still had the issue.
Thank you for your report!
However, this issue is Invalid.
Your game, launcher or server is modified.
If you can reproduce the issue in a vanilla environment, please recreate the issue.
Any non-standard client/server/launcher build needs to be taken up with the appropriate team, not Mojang.
Any plugin issues need to be addressed to the creator of the plugin or resource pack.
If you have problems on large servers, such as The Hive and Hypixel, please contact them first as they run modified server software.
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Can you provide the world seed, coordinates, and version you originally created the world?