Not a developer here....however, I do have some experience with staff hierarchies. My guess is that someone flagged the email for Jobs. Maybe at the same time brought in an Apple developer to look at the app - perhaps the same one who is/will be looking at the supposed bug.
Jobs would have been briefed by the Apple developer, who would have made themselves familiar with the proposed app. They likely would have pointed out the workaround - and Jobs would have then called the app's developer, explained company policy, and then mentioned the suggested workaround.
Jobs does not need to know how every single thing at Apple works, but he will have a really good briefing before venturing into anything.
I wonder if the app is considered to be otherwise a shining example of what Apple would like to see, so that extra effort was made to keep the developer happy.