In February of 2005 myself and a friend crossed into Mexico at the Naco crossing(south of Bisbee). The immigration and vehicle registration offices were just around the corner from each other. In addition at the vehicle office they made all copies on their copy machine and did not charge us anything. We also paid all fees at that office and took the receipt back to immigration who issued us the travel permits. It took about 30 minutes.
We later took the ferry to Baja Sur from Topolobampo to La Paz and was not asked about travel permits. When we came back from Santa Rosalita to Los Mochus on that ferry we were not asked for anything except cash. They would not accept credit cards. (the ferry from Topo. to La Paz took credit cards). We came back through Naco on the way home and turned in our vehicle permits. (5 minutes??). jim