I think that only applies to air crossings.
At least w/ Canada there's an agreement for the Canucks to tell CBR that you've left the US (Source: I tried to surrender my i-94 at the US side of the border. The guy told me to give it to Canadians). Not hard to envision another agreement on the Mexican side
Not sure why the US needs to make a big deal out of it with biometric scans instead of the tried-and-true option of a little man in a box stamping your passport.