I don't see the connection.

Your point seems to be about the chosen operating software's security model. I agree that flexibility here is woefully lacking in all the major desktop OSes today.

However, the original concern in this case seems to be about being able to choose the basic operating software for the system itself, which is an orthogonal issue to the one you're raising as I understand your comment.

The lack of security for major OSes and the exploits that were caused by the freedom to install software from any source, which lead to the said software being able to do anything in user's name, is what lead to solutions like application stores and things like SGX.

Because the average Joe and Jane users don't understand anything about security, and prefer to loose freedom than having their computer exploited.

But the modern measures about locking down the hardware itself, which are the subject of this discussion, have nothing to do with app sandboxing and app stores...