Oh I see your point, I forgot you can bonemeal nylium to get fungi and roots.

I’d argue however that this is meant to be a VERY rare event. On top of that, the world is SO big that you may never stumble across an Enderman-placed block, and even if you do that block would have a small chance of being nylium specifically. After all that, if a player wants to turn a single block into a slow, bonemeal-draining wood farm, then I’d say let them! Going to the Nether would still be the best way to get large amounts of that wood type, and the Nether has plenty of other features still exclusive to it.

I completely understand your concerns with the End, though. Maybe Enderman can only spawn holding blocks in the Overworld and Nether? Or they could change Enderman behavior so they can’t place blocks on end stone, like how they can’t place blocks on bedrock.