That's part of a factory recovery mechanism, basically. The system looks for Start+Select+X+Power and the magnet to be detected and it'll immediately fail over to booting from the DS slot.
It pretty much has to be either a service mode or a developer back door. I'd love to know for sure. Maybe a leak some day will satisfy my curiosity.
In the presentation made when it was discovered[0] they said: “The NTR cartridge was likely meant to be used for either the factory setup or as a means of recovering bricked NANDs. However, we'll never know for sure.”