The Streaming Instability (SI) is a mechanism to concentrate solids in protoplanetary disks. Nonlinear particle clumping from the SI can trigger gravitational collapse into planetesimals. To better understand the numerical robustness of the SI, we perform a suite of vertically-stratified 3D simulations with fixed physical parameters known to produce strong clumping. We vary the numerical implementation, namely the computational domain size and the vertical boundary conditions (vBCs), comparing newly-implemented outflow vBCs to the previously-used periodic and reflecting vBCs. We find strong particle clumping by the SI is mostly independent of the vBCs. However, peak particle densities are higher in larger simulation domains due to a larger particle mass reservoir. We report SI-triggered zonal flows, i.e., azimuthally-banded radial variations of gas pressure. These structures have low amplitudes, insufficient to halt particle radial drift, confirming that particle trapping in gas pressure maxima is not the mechanism of the SI. We find that outflow vBCs produce artificially large gas outflow rates at vertical boundaries. However, the outflow vBCs reduce artificial reflections at vertical boundaries, allowing more particle sedimentation, and showing less temporal variation and better convergence with box size. The radial spacing of dense particle filaments is $sim0.15$ gas scale heights ($H$) for all vBCs, which sets the feeding zone for planetesimal growth in self-gravitating simulations. Our results validate the use of the outflow vBCs in SI simulations, even with vertical boundaries close ($leq 0.4H$) to the disk midplane. Overall, our study demonstrates the numerical robustness of nonlinear particle clumping by the SI.
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