Standard gate-level transpilation introduces significant physical noise and overhead for high-precision quantum algorithms, such as the Quantum Singular Value Transformation (QSVT), on near-term trapped-ion hardware. Current compilers treat quantum operations as discrete units, forcing the physical control layer to execute highly fragmented laser pulses. To address this hardware-software disconnect, this work introduces a holistic pulse synthesis strategy that bypasses discrete gate-stitching to compile algorithms directly into continuous compound pulse gadgets. As a proof-of-concept, we target Hamiltonian simulation of the $H_2$ molecule, block-encoding the problem into a QSVT circuit to approximate the time-evolution operator $U = e^{-i H t}$ across 3 computational ions (2 system, 1 ancilla). We utilize the Gradient Ascent Pulse Engineering (GRAPE) algorithm to generate these compound gadgets and evaluate our methodology using noisy Lindblad master equation simulations. Preliminary observations indicate that the proposed strategy achieves significant temporal compression, reducing the total pulse schedule duration compared to standard compilers. Furthermore, synthesizing operations holistically eliminates the control-layer latency associated with discrete pulse lookup overhead. By streamlining the physical control schedule, this methodology offers a promising pathway to execute operations faster, highlighting the potential for compound gadgets to increase the computational depth achievable within fundamental $T_2$ decoherence limits.

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