In this study the isogeometric B-Rep mortar-based mapping method for geometry models stemming directly from Computer-Aided Design (CAD) is systematically augmented and applied to partitioned Fluid-Structure Interaction (FSI) simulations. Thus, the newly proposed methodology is applied to geometries described by their Boundary Representation (B-Rep) in terms of trimmed multipatch Non-Uniform Rational B-Spline (NURBS) discretizations as standard in modern CAD. The proposed isogeometric B-Rep mortar-based mapping method is herein extended for the transformation of fields between a B-Rep model and a low order discrete surface representation of the geometry which typically results when the Finite Volume Method (FVM) or the Finite Element Method (FEM) are employed. This enables the transformation of such fields as tractions and displacements along the FSI interface when Isogeometric B-Rep Analysis (IBRA) is used for the structural discretization and the FVM is used for the fluid discretization. The latter allows for diverse discretization schemes between the structural and the fluid Boundary Value Problem (BVP), taking into consideration the special properties of each BVP separately while the constraints along the FSI interface are satisfied in an iterative manner within partitioned FSI. The proposed methodology can be exploited in FSI problems with an IBRA structural discretization or to FSI problems with a standard FEM structural discretization in the frame of the Exact Coupling Layer (ECL) where the interface fields are smoothed using the underlying B-Rep parametrization, thus taking advantage of the smoothness that the NURBS basis functions offer. All new developments are systematically investigated and demonstrated by FSI problems with lightweight structures whereby the underlying geometric parametrizations are directly taken from real-world CAD models, thus extending IBRA into coupled problems of the FSI type.