All of the components of the LSST subsystems (Telescope and Site, Camera, and Data Management) are in production. The major systems engineering challenges in this early construction phase are establishing the final technical details of the observatory, and properly evaluating potential deviations from requirements due to financial or technical constraints emerging from the detailed design and manufacturing process. To meet these challenges, the LSST Project Systems Engineering team established an Integrated Modeling (IM) framework including (i) a high fidelity optical model of the observatory, (ii) an atmospheric aberration model, and (ii) perturbation interfaces capable of accounting for quasi static and dynamic variations of the optical train. The model supports the evaluation of three key LSST Measures of Performance: image quality, ellipticity, and their impact on image depth. The various feedback loops improving image quality are also included. The paper shows application examples, as an update to the estimated performance of the Active Optics System, the determination of deployment parameters for the wavefront sensors, the optical evaluation of the final M1M3 surface quality, and the feasibility of satisfying the settling time requirement for the telescope structure.