They are... But not really. The machine will flag you if you are going through with your shoes on and something is off about them. The only thing that's different is it is easier to swab them if they think something may be off about them.
Which if you went through the body scanner and they thought something was off, they are going to ask you to step aside and remove them to be swabbed.
(Hence why anyone who applies for TSA pre check, could already keep their shoes on)