Trapped-ion Quantum Charge-Coupled Devices (QCCD) are a leading contender for quantum computing, but their scalability is constrained by control wiring and electronics. Wiring using Integrated Switching Electronics (WISE), a recently proposed QCCD architecture, reduces wiring through multiplexing and integrated switching hardware. However, this leaves an execution model with limited parallelism and limited flexibility in ion movement. Further, these devices need to be paired with a quantum error correction (QEC) code to enable fault-tolerant quantum computation (FTQC). Can WISE architectures efficiently support FTQC requirements? Which QEC choices, device and control parameters are practical? We present WISER, a cross-layer design-space exploration framework for trapped-ion systems with multiplexed control. WISER combines a WISE-specific SAT-based compiler, a physics-informed noise model and logical-memory simulation to estimate logical error rates, logical clock speeds and control power across hardware parameters and QEC families. Its compiler reduces routing time by 2.6--18.8× relative to a greedy WISE-compatible baseline. Our analysis provides concrete design guidance. Two-ion traps with 16-way multiplexing, 8× lower than the original WISE proposal, give the fastest logical clock that meets our reliability and cold-stage power targets. With current hardware parameters, the distance-7 surface code is the only evaluated code to meet our early-FTQC screen, at 4.58 Hz and 2.04 W of DAC power per logical qubit. At this operating point, ion transport and recooling take 94--96% of the WISE cycle, and even without them sample-and-hold electrode charging leaves millisecond-scale syndrome-extraction rounds.