Like the freedom to run my own choice of operating system?

Or the freedom to reset my device to a known-good state from read-only media so I know it's safe to use again after potentially being compromised through these slightly-too-clever new reprogrammable systems?

No the freedom that any programm has full rights of $HOME, to access the network, to manipulate everything that the user under it runs also can.

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...

Which freedom exactly was abused?

Edit: also if something can be abused it is not a freedom but a granted temporary privilege.

To run software with full rights of $HOME or similar, acess the network and manipulate PC contents without the user knowing about it.