You can hold "Ctrl" then middle click on a chest to get a chest with NBT. This works as intended. But you can middle click on an ender chest.
What I expected was:
The ender chest should not have any NBT.
Steps to reproduce:
1. Place down an ender chest.
2. Put something in it.
3. Hold "Ctrl" then middle click on it.
4. Remove things inside the ender chest.
5. Place down the ender chest with "NBT".
Ender chest's don't save their items in their NBT data. That's stored in the player's file.