I was under the impression that no unsigned script should be loaded if the script editor has not been activated. I was, of course, wrong

Here is what is going on:
If you have any unsigned scripts that begin with a '!' they will be loaded regardless of whether they are signed or unsigned. Scripts that begin with a ! are special cases and will always be run, signed or not.
However, loading an unsigned script simply because it begins with a '!' will kick your game into running in *modified* mode. You can check the player stats at the bottom to verify this. This is exactly the same as if you had enabled the script editor to get your game into modified mode.
Once your game is running in modified mode, upon the next game load, all unsigned scripts will be run, since running in modified mode is equivalent to having activated the script editor.
Make sense?
So under normal circumstances, unless you have a script that begins with an !, unsigned setup/init scripts should not be running in an unmodified game. This is how it worked in X2 as well.
It is suggested that community modders do NOT EVER start a script with !.
Since it can cause a cascading effect, loading unsigned scripts into a game where the script editor has not been expressly activated.
Hope that clears things up.
Cheers.