The recent emergence of planar transport systems necessitates re-evaluation of Flexible Manufacturing Systems (FMS) to address the simultaneous scheduling of internal logistics and production operations. By operating on a tile-based planar grid, these systems allow independent movers full two-dimensional freedom, mitigating inefficiencies inherent to traditional sequential lines. This paper applies a planar FMS framework to a real-world use case in the pharmaceutical industry: the automated production of personalized drugs. Implementing this system requires solving optimization problems at both tactical and operational levels. The tactical level involves decisions regarding production line layout and the positioning of drug dispensers. A Mixed-Integer Quadratic Programming model is utilized for the packing problem to exploit drug co-occurrence patterns found in historical patient data. Subsequently, we solve the placement problem - a bi-level problem combining an assignment problem with Shortest Hamiltonian paths with neighborhoods - to arrange dispensers in a layout minimizing expected travel distances. The operational level is encountered daily, scheduling individual movers to process new orders as quickly as possible. This scheduling problem is formulated using Constraint Programming, modeling movers as reservoir resources to ensure order completeness, complemented by a routing phase using an iterative conflict-resolution mechanism and DAG-based reasoning to convert schedules into conflict-free paths. Evaluation using real-world prescription data for 40 drugs shows the framework scales efficiently across several layout topologies for up to 500 orders, with schedules that are highly effective and computationally tractable for daily operations.