Not sure if you've bought alcohol lately, but at most large grocers near me, they're scanning licenses now instead of just verifying the birth date - and I'm pretty confident those scans aren't just checking the birthdate and then deleting all record of the interaction..
Not sure where you are but no one has ever done that to me. I usually would go through self checkouts so someone just comes over, takes a quick look at my drivers licence, and puts in their employee id into the machine to authorise it.
I'm in the midwest, but at several large chains with hundreds of locations, even at the self-checkout when you buy booze, it flashes the little 'attendant needed' sign, the person comes over, scans their badge, takes your ID to do a 1 second look, and then scans it on the same barcode reader you use for your box of cereal.
They can deny you service at any time, but it's unlikely they will do so if you present a valid ID, even if it's not machine-readable. Not every driver license can be easily scanned, so in that respect it's no different from a passport.