This PBS NewsHour story by Miles O'Brien (which I worked on, as a shooter/producer) breaks it down.
Here's the deal: The devices branded "Rapiscan" that look like a blue box are the backscatter devices. These are the controversial devices that emit ionizing radiation (though exactly how much, and whether that's safe, is debatable). They also store and transmit very clearly invasive images of your naked body.
The millimiter wave machines made by L3 that look like a Tardis do not emit ionizing radiation. By all means, go ahead and opt out of those too, if privacy and civil liberties are your primary concern and you believe these searches violate your rights. But the Rapiscan devices are the ones that cause radiation exposure health concerns, not the L3 millimeter wave devices.
Again, the Rapiscan backscatter machines (which cost our government around $200K each) are the ones that emit ionizing radiation and create an invasively clear image of your body ("pornoscanners"). The L3 millimeter wave devices do not.
As ProPublica reports, the Rapiscan devices are quietly disappearing from major airports in the US and showing up in storage warehouses. Nobody in the civilian world is really certain what's going on, but it does appear that the TSA/DHS are retiring the Rapiscan devices for which we taxpayers paid billions.
(Thanks for the explainer, Miles O'Brien!)