It still does. The only thing is we've distinguished physical ownership and mere physical possession.

It is a feature that if I leave my personal laptop at my desk at work while using the bathroom, my IT department can't rootkit it. It is an improvement to my freedom - both my computing freedom and my physical freedom - if I can leave a laptop in my hotel room while seeing tourist sights. It protects me from the government if a border control agent looking through my bag, or a cop who's seized my laptop, can't get in. (The iPhone is an existence proof that such defense against the government is possible, and it's weird that the usually pro-personal-liberty free software crowd hasn't decided that a free software implementation of the same thing is critically important.)

Of course software freedom requires access control. My freedom over my possessions involves other people's lack of freedom over my possessions. I can't make sure my computer is running the code I want it to if everyone else can make my computer run the code they want it to. This control is essential liberty; pretending that anyone with physical access is an owner because it's easier than crypto and key management has been decades of temporary convenience, and I'm glad it's coming to an end.

I can turn secure boot on and off with an admin password, which I set when I first booted the machine because that's what demonstrates physical ownership and not mere possession. (And systems that don't permit me to do so, like Microsoft or Apple ARM devices, are in fact an affront to software freedom.) But nobody else can.