Novel aircraft configurations require closer integration of design and analysis models to enable rapid iteration across disciplines. For structural modelling of the aircraft skin, isogeometric B-Rep analysis (IBRA) of shell structures offers an effective solution by enabling direct computation on CAD geometry without intermediate meshing [1]. To achieve a lightweight design, the aircraft fuselage skin is reinforced with stiffeners, which conventionally consist of orthogonally arranged stringer and frame elements (orthogrids). However, especially for unconventional fuselage concepts, alternative stiffener layouts based on Non-Uniform Rational BSplines (NURBS) can lead to favorable weight reductions. Research by [2] has demonstrated how nonlinear isogeometric spatial Bernoulli beams can be embedded in shell elements using nested parameterization. The mesh-independent strong coupling makes this approach well suited for stiffener layout optimization. In the present study, this method is implemented in the Kratos Multiphysics framework [3] for stiffened laminated composite Kirchhoff-Love shells. It is then applied to find the optimal stiffener layout for an unconventional rear fuselage design with highly integrated engines. The stiffener layout is optimized for both compliance minimization and buckling eigenvalue maximization using Bayesian optimization. The optimization is followed by a sizing loop to estimate the influence of engine integration on structural weight early in the design process. Finally, results are compared against a density-based topology optimization baseline. [1] T. Teschemacher, A.M. Bauer, T. Oberbichler, Realization of CAD-integrated shell simulation based on isogeometric B-Rep analysis, Advanced Modeling and Simulation in Engineering Sciences, Vol. 5, 19, 2019. [2] A.M. Bauer, M. Breitenberger, B. Philipp, R. W¨uchner, K.-U. Bletzinger, Embedded structural entities in NURBS-based isogeometric analysis, Computer Methods in Applied Mechanics and Engineering, Vol. 325, pp. 198–218, 2017. [3] V. Mataix Ferr´andiz, P. Bucher, R. Zorrilla, et al., KratosMultiphysics/Kratos: Release v10.2.3, Zenodo, 2025, https://doi.org/10.5281/zenodo.15687676.