1. The lender should notate on the application that he/she obtained joint intent. 2. No - and why would they use 2 applications? You would still have to ask the question and notate the answer.
In a previous life the mortgage company would do two applications if the applicants weren't married - however that is treating applicants different under marital status.
When we have 2 applications for 1 request for credit, we have both applicants sign a separate piece of paper acknowledging intent to apply jointly. Examiners have never indicated a problem with it.