For integrating a LINK cartridge that is certified for pipelines and controllers into a system using the Storefront Reference Architecture (SFRA), which primarily uses scripts instead of the older pipeline technology, the architect should update the job pipelines to work as custom job steps. This approach allows the existing LINK cartridge functionalities to be maintained while making them compatible with the SFRA framework. Custom job steps enable more flexibility and the ability to leverage the full capabilities of SFRA, ensuring that the jobs run correctly within the newer architecture.