There is still the underlying idea that the scanner is producing an image of your naked body under your clothing. True, with ATR, the screener is no longer seeing that image, and in theory, it is only being saved in memory temporarily for the software to process it, but nevertheless, an under-the-clothing image is being produced. As an extreme example, would it still be okay if you had to go into a private cell and strip down, and have several cameras take pictures of you to be processed, as long as those images were not saved and not viewed by a screener?

With a frisk, no one is seeing under your clothes, and there is no image to be potentially saved.

Now whether having a machine take an under-the-clothing image is more or less invasive than a government employee running his or her hands up and down your clothing is subject to debate. Both are disgusting options.