Script preferences are saved in the registry as global preferences; they have their own registry subkey. Thus not per-user...
If this is going to be changed, it means a very big radical change. So I very much doubt this will happen any time soon.
Moreover, there are reasons why it is the way it is. For starters, scripts are executed even before a user signs in. And they do not stop when a user signs out. So it makes not much sense to store script preferences per-user either.
Although it might have some benefits for some scripts, for others it is simply not logical to store them per-user.
If you want scripts to be executed depending on who signed in, you must alter the script in such a way that it checks upon who has signed in, and only executes its functions depending on that, like you requested
here.
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