Yea, it actually would.
To avoid this, you can make a spell book and add the endurance aura in there.
Then you have to add the spell book to the unit instead (the levels still have to be applied on the endurance aura which is added automatically via the spell book).
This will make the endurance aura be added in a subset hidden on the command chart of the unit.
The only way to access it is by clicking (or hotkey) on the spell book.
If you disable the spell book via triggers, you still make use of the endurance aura but do not use the spell book.
Make a trigger that runs on map init that loops through all players in the game.
Then you disable the spell book ability for the picked players.
(You can add additional spell books to this trigger if any.)